diff --git a/biolink-model.yaml b/biolink-model.yaml index da453c72a..28a336ba4 100644 --- a/biolink-model.yaml +++ b/biolink-model.yaml @@ -7054,8 +7054,6 @@ classes: - STY:T075 # Drug Delivery Device - STY:T203 - # Biomedical or Dental Material - - STY:T122 diagnostic aid: is_a: named thing diff --git a/project/jsonld/biolink_model.context.jsonld b/project/jsonld/biolink_model.context.jsonld index cc2f24ed9..b42577433 100644 --- a/project/jsonld/biolink_model.context.jsonld +++ b/project/jsonld/biolink_model.context.jsonld @@ -1,7 +1,7 @@ { "comments": { "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2024-07-25T17:45:05", + "generation_date": "2024-07-25T17:51:03", "source": "biolink_model.yaml" }, "@context": { diff --git a/project/jsonld/biolink_model.jsonld b/project/jsonld/biolink_model.jsonld index 654d1d242..08083f2f3 100644 --- a/project/jsonld/biolink_model.jsonld +++ b/project/jsonld/biolink_model.jsonld @@ -24526,8 +24526,7 @@ "UMLSSG:DEVI", "STY:T074", "STY:T075", - "STY:T203", - "STY:T122" + "STY:T203" ], "is_a": "NamedThing", "slots": [ @@ -35037,9 +35036,9 @@ ], "metamodel_version": "1.7.0", "source_file": "biolink_model.yaml", - "source_file_date": "2024-07-25T17:45:00", - "source_file_size": 393015, - "generation_date": "2024-07-25T17:45:06", + "source_file_date": "2024-07-25T17:50:59", + "source_file_size": 392960, + "generation_date": "2024-07-25T17:51:05", "@type": "SchemaDefinition", "@context": [ "project/jsonld/biolink_model.context.jsonld", diff --git a/project/owl/biolink_model.owl.ttl b/project/owl/biolink_model.owl.ttl index fa348708d..b71118439 100644 --- a/project/owl/biolink_model.owl.ttl +++ b/project/owl/biolink_model.owl.ttl @@ -123,10 +123,10 @@ biolink:HospitalizationOutcome a owl:Class ; biolink:MappingCollection a owl:Class ; rdfs:label "mapping collection" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:PredicateMapping ; owl:onProperty biolink:predicate_mappings ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PredicateMapping ; + owl:minCardinality 0 ; owl:onProperty biolink:predicate_mappings ], linkml:ClassDefinition ; skos:definition "A collection of deprecated mappings." ; @@ -2601,16 +2601,16 @@ biolink:AccessibleDnaRegion a owl:Class ; rdfs:label "accessible dna region" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:OntologyClass ], biolink:RegulatoryRegion ; skos:altLabel "atac-seq accessible region", "dnase-seq accessible region" ; @@ -2656,32 +2656,32 @@ biolink:AccessibleDnaRegion a owl:Class ; biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity ontogenic association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], biolink:AnatomicalEntityToAnatomicalEntityAssociation ; skos:definition "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ; skos:inScheme . @@ -2689,6 +2689,12 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity part of association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; @@ -2696,25 +2702,19 @@ biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a owl:Class ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:AnatomicalEntityToAnatomicalEntityAssociation ; skos:definition "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; skos:inScheme . @@ -2733,13 +2733,13 @@ biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; owl:allValuesFrom biolink:BehavioralFeature ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:allValuesFrom biolink:Behavior ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Behavior ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -2748,8 +2748,8 @@ biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], biolink:Association ; skos:definition "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." ; skos:inScheme . @@ -2777,17 +2777,17 @@ biolink:BioticExposure a owl:Class ; biolink:Book a owl:Class ; rdfs:label "book" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], + owl:minCardinality 0 ; + owl:onProperty biolink:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:type ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:type ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:id ], @@ -2805,10 +2805,10 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "case to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:someValuesFrom biolink:CaseToEntityAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CaseToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], biolink:Association ; skos:definition "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype." ; skos:inScheme . @@ -2816,11 +2816,14 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; biolink:CausalGeneToDiseaseAssociation a owl:Class ; rdfs:label "causal gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], @@ -2828,17 +2831,14 @@ biolink:CausalGeneToDiseaseAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:GeneToDiseaseAssociation ; skos:inScheme . @@ -2931,20 +2931,20 @@ biolink:Cell a owl:Class ; biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "cell line as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:CellLine ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; skos:inScheme . @@ -2957,167 +2957,167 @@ biolink:CellLineToEntityAssociationMixin a owl:Class ; biolink:ChemicalAffectsGeneAssociation a owl:Class ; rdfs:label "chemical affects gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:causal_mechanism_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; + owl:minCardinality 0 ; owl:onProperty biolink:causal_mechanism_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:anatomical_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_part_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)" ; skos:inScheme . @@ -3129,25 +3129,25 @@ biolink:ChemicalEntityAssessesNamedThingAssociation a owl:Class ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], @@ -3157,40 +3157,40 @@ biolink:ChemicalEntityAssessesNamedThingAssociation a owl:Class ; biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ; rdfs:label "chemical entity or gene or gene product regulates gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "A regulatory relationship between two genes" ; @@ -3200,106 +3200,106 @@ biolink:ChemicalGeneInteractionAssociation a owl:Class ; rdfs:label "chemical gene interaction association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; + owl:minCardinality 0 ; owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:object_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_part_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; owl:onProperty biolink:subject_derivative_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], biolink:Association ; skos:definition "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; skos:exactMatch SIO:001257 ; @@ -3313,15 +3313,15 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; skos:definition "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect." ; skos:inScheme . @@ -3349,38 +3349,38 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; rdfs:label "chemical to chemical derivation association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:catalyst_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:MacromolecularMachineMixin ; owl:onProperty biolink:catalyst_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:catalyst_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], biolink:ChemicalToChemicalAssociation ; skos:definition "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 catalyst qualifier P" ; skos:inScheme . @@ -3388,13 +3388,10 @@ biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "chemical to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; @@ -3402,6 +3399,9 @@ biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], biolink:Association ; skos:definition "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype." ; skos:inScheme ; @@ -3410,16 +3410,10 @@ biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; biolink:ChemicalToPathwayAssociation a owl:Class ; rdfs:label "chemical to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Pathway ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -3427,6 +3421,12 @@ biolink:ChemicalToPathwayAssociation a owl:Class ; [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Pathway ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], @@ -3464,10 +3464,10 @@ biolink:ChiSquaredAnalysisResult a owl:Class ; biolink:ClinicalFinding a owl:Class ; rdfs:label "clinical finding" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:ClinicalAttribute ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ClinicalAttribute ; + owl:minCardinality 0 ; owl:onProperty biolink:has_attribute ], biolink:PhenotypicFeature ; skos:definition "this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations." ; @@ -3479,10 +3479,10 @@ biolink:ClinicalMeasurement a owl:Class ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_attribute_type ], biolink:ClinicalAttribute ; skos:definition "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot." ; @@ -3536,38 +3536,38 @@ biolink:ConceptCountAnalysisResult a owl:Class ; biolink:ContributorAssociation a owl:Class ; rdfs:label "contributor association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualifiers ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:qualifiers ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:InformationContentEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:InformationContentEntity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Agent ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualifiers ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; skos:inScheme . @@ -3575,29 +3575,29 @@ biolink:ContributorAssociation a owl:Class ; biolink:CorrelatedGeneToDiseaseAssociation a owl:Class ; rdfs:label "correlated gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], biolink:GeneToDiseaseAssociation ; skos:inScheme . @@ -3615,10 +3615,10 @@ biolink:DiseaseOrPhenotypicFeatureExposure a owl:Class ; rdfs:label "disease or phenotypic feature exposure" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ExposureEvent ], + owl:someValuesFrom biolink:PathologicalEntityMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PathologicalEntityMixin ], + owl:someValuesFrom biolink:ExposureEvent ], biolink:Attribute ; skos:definition "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer." ; skos:inScheme . @@ -3626,17 +3626,14 @@ biolink:DiseaseOrPhenotypicFeatureExposure a owl:Class ; biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a owl:Class ; rdfs:label "disease or phenotypic feature to genetic inheritance association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneticInheritance ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], @@ -3644,8 +3641,11 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneticInheritance ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." ; skos:inScheme . @@ -3653,13 +3653,13 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a owl:Class ; biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a owl:Class ; rdfs:label "disease or phenotypic feature to location association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -3683,11 +3683,26 @@ biolink:DiseaseToExposureEventAssociation a owl:Class ; biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "disease to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:allValuesFrom biolink:Onset ; owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:FrequencyQuantifier ], @@ -3697,27 +3712,12 @@ biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], biolink:Association ; skos:closeMatch dcid:DiseaseSymptomAssociation ; skos:definition "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; @@ -3769,10 +3769,10 @@ biolink:DrugToEntityAssociationMixin a owl:Class ; biolink:DrugToGeneAssociation a owl:Class ; rdfs:label "drug to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; @@ -3817,58 +3817,58 @@ biolink:DrugToGeneInteractionExposure a owl:Class ; biolink:DruggableGeneToDiseaseAssociation a owl:Class ; rdfs:label "druggable gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:DruggableGeneCategoryEnum ; owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_evidence ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], biolink:GeneToDiseaseAssociation ; skos:inScheme . biolink:EntityToDiseaseAssociation a owl:Class ; rdfs:label "entity to disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; + owl:onProperty biolink:clinical_approval_status ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:clinical_approval_status ], + [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:max_research_phase ], + owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; owl:allValuesFrom biolink:MaxResearchPhaseEnum ; owl:onProperty biolink:max_research_phase ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; - owl:onProperty biolink:clinical_approval_status ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:clinical_approval_status ], + owl:onProperty biolink:max_research_phase ], biolink:Association ; skos:inScheme . @@ -3893,17 +3893,17 @@ biolink:EntityToPhenotypicFeatureAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:max_research_phase ], + owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; + owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MaxResearchPhaseEnum ; + owl:maxCardinality 1 ; owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; - owl:onProperty biolink:clinical_approval_status ], + owl:allValuesFrom biolink:MaxResearchPhaseEnum ; + owl:onProperty biolink:max_research_phase ], biolink:Association ; skos:inScheme . @@ -3944,22 +3944,22 @@ biolink:Event a owl:Class ; biolink:ExonToTranscriptRelationship a owl:Class ; rdfs:label "exon to transcript relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:Transcript ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Exon ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Exon ; owl:onProperty biolink:subject ], biolink:SequenceFeatureRelationship ; skos:definition "A transcript is formed from multiple exons" ; @@ -3971,23 +3971,23 @@ biolink:ExposureEventToOutcomeAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:temporal_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:temporal_context_qualifier ], + owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:time_type ; - owl:onProperty biolink:temporal_context_qualifier ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:maxCardinality 1 ; owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:population_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:temporal_context_qualifier ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin ], + owl:allValuesFrom biolink:time_type ; + owl:onProperty biolink:temporal_context_qualifier ], biolink:Association ; skos:definition "An association between an exposure event and an outcome." ; skos:inScheme . @@ -4000,12 +4000,12 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a owl:Class ; [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ExposureEvent ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ExposureEvent ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; skos:inScheme . @@ -4063,176 +4063,176 @@ biolink:Fungus a owl:Class ; biolink:GeneAffectsChemicalAssociation a owl:Class ; rdfs:label "gene affects chemical association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:anatomical_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:object_derivative_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:object_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:subject_aspect_qualifier ], biolink:Association ; skos:definition "Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)" ; skos:inScheme . @@ -4240,61 +4240,61 @@ biolink:GeneAffectsChemicalAssociation a owl:Class ; biolink:GeneAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "gene as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], biolink:GeneToDiseaseAssociation ; skos:inScheme . biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; rdfs:label "gene has variant that contributes to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:GeneToDiseaseAssociation ; skos:inScheme . @@ -4562,50 +4562,50 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; rdfs:label "gene to expression site association" ; rdfs:seeAlso ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:LifeStage ; owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:quantifier_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; skos:editorialNote "TBD: introduce subclasses for distinction between wild-type and experimental conditions?" ; @@ -4617,14 +4617,14 @@ biolink:GeneToGeneCoexpressionAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneExpressionMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneExpressionMixin ], biolink:GeneToGeneAssociation ; skos:definition "Indicates that two genes are co-expressed, generally under the same conditions." ; skos:inScheme . @@ -4633,30 +4633,30 @@ biolink:GeneToGeneFamilyAssociation a owl:Class ; rdfs:label "gene to gene family association" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneFamily ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; @@ -4665,32 +4665,32 @@ biolink:GeneToGeneFamilyAssociation a owl:Class ; biolink:GeneToGeneHomologyAssociation a owl:Class ; rdfs:label "gene to gene homology association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], biolink:GeneToGeneAssociation ; skos:definition "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; skos:inScheme . @@ -4698,32 +4698,32 @@ biolink:GeneToGeneHomologyAssociation a owl:Class ; biolink:GeneToGeneProductRelationship a owl:Class ; rdfs:label "gene to gene product relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneProductMixin ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneProductMixin ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], biolink:SequenceFeatureRelationship ; skos:definition "A gene is transcribed and potentially translated to a gene product" ; skos:inScheme . @@ -4731,22 +4731,22 @@ biolink:GeneToGeneProductRelationship a owl:Class ; biolink:GeneToGoTermAssociation a owl:Class ; rdfs:label "gene to go term association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:object ], biolink:FunctionalAssociation ; skos:altLabel "functional association" ; @@ -4756,23 +4756,23 @@ biolink:GeneToGoTermAssociation a owl:Class ; biolink:GeneToPathwayAssociation a owl:Class ; rdfs:label "gene to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Pathway ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Pathway ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], @@ -4783,20 +4783,20 @@ biolink:GeneToPathwayAssociation a owl:Class ; biolink:GeneToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "gene to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:PhenotypicFeature ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], @@ -4804,7 +4804,7 @@ biolink:GeneToPhenotypicFeatureAssociation a owl:Class ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; skos:exactMatch WBVocab:Gene-Phenotype-Association ; @@ -4813,14 +4813,14 @@ biolink:GeneToPhenotypicFeatureAssociation a owl:Class ; biolink:Genome a owl:Class ; rdfs:label "genome" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence ], biolink:BiologicalEntity ; skos:closeMatch dcid:GenomeAssemblyUnit ; skos:definition "A genome is the sum of genetic material within a cell or virion." ; @@ -4833,22 +4833,22 @@ biolink:GenomicBackgroundExposure a owl:Class ; rdfs:label "genomic background exposure" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ThingWithTaxon ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:ThingWithTaxon ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneGroupingMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ExposureEvent ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence ], biolink:Attribute ; skos:definition "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." ; skos:inScheme . @@ -4856,19 +4856,19 @@ biolink:GenomicBackgroundExposure a owl:Class ; biolink:GenotypeAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "genotype as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], biolink:GenotypeToDiseaseAssociation ; skos:inScheme . @@ -4876,7 +4876,7 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a owl:Class ; biolink:GenotypeToGeneAssociation a owl:Class ; rdfs:label "genotype to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -4888,20 +4888,20 @@ biolink:GenotypeToGeneAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ; skos:inScheme . @@ -4909,32 +4909,32 @@ biolink:GenotypeToGeneAssociation a owl:Class ; biolink:GenotypeToGenotypePartAssociation a owl:Class ; rdfs:label "genotype to genotype part association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:Genotype ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Any association between one genotype and a genotypic entity that is a sub-component of it" ; skos:inScheme . @@ -4942,8 +4942,8 @@ biolink:GenotypeToGenotypePartAssociation a owl:Class ; biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "genotype to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], @@ -4953,17 +4953,17 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; @@ -4974,30 +4974,30 @@ biolink:GenotypeToVariantAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], biolink:Association ; skos:definition "Any association between a genotype and a sequence variant." ; skos:inScheme . @@ -5036,14 +5036,14 @@ biolink:GeographicExposure a owl:Class ; biolink:GeographicLocationAtTime a owl:Class ; rdfs:label "geographic location at time" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:timepoint ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:allValuesFrom biolink:time_type ; owl:onProperty biolink:timepoint ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:timepoint ], biolink:GeographicLocation ; skos:definition "a location that can be described in lat/long coordinates, for a particular time" ; skos:inScheme . @@ -5064,13 +5064,13 @@ biolink:Haplotype a owl:Class ; rdfs:label "haplotype" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:GenomicEntity ], biolink:BiologicalEntity ; skos:definition "A set of zero or more Alleles on a single instance of a Sequence[VMC]" ; skos:exactMatch , @@ -5101,31 +5101,31 @@ biolink:Human a owl:Class ; biolink:InformationContentEntityToNamedThingAssociation a owl:Class ; rdfs:label "information content entity to named thing association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." ; @@ -5205,14 +5205,14 @@ biolink:MacromolecularComplex a owl:Class ; biolink:MacromolecularMachineToBiologicalProcessAssociation a owl:Class ; rdfs:label "macromolecular machine to biological process association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:allValuesFrom biolink:BiologicalProcess ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], @@ -5223,17 +5223,17 @@ biolink:MacromolecularMachineToBiologicalProcessAssociation a owl:Class ; biolink:MacromolecularMachineToCellularComponentAssociation a owl:Class ; rdfs:label "macromolecular machine to cellular component association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:CellularComponent ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:CellularComponent ; + owl:onProperty biolink:object ], biolink:FunctionalAssociation ; skos:definition "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component." ; skos:inScheme . @@ -5241,17 +5241,17 @@ biolink:MacromolecularMachineToCellularComponentAssociation a owl:Class ; biolink:MacromolecularMachineToMolecularActivityAssociation a owl:Class ; rdfs:label "macromolecular machine to molecular activity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], biolink:FunctionalAssociation ; skos:definition "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution." ; skos:inScheme . @@ -5259,32 +5259,32 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a owl:Class ; biolink:MaterialSampleDerivationAssociation a owl:Class ; rdfs:label "material sample derivation association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:allValuesFrom biolink:predicate_type ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MaterialSample ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:MaterialSample ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "An association between a material sample and the material entity from which it is derived." ; skos:inScheme . @@ -5351,20 +5351,20 @@ biolink:MolecularActivityToChemicalEntityAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; skos:inScheme . @@ -5372,23 +5372,23 @@ biolink:MolecularActivityToChemicalEntityAssociation a owl:Class ; biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ; rdfs:label "molecular activity to molecular activity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularActivity ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; skos:inScheme . @@ -5396,32 +5396,32 @@ biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ; biolink:MolecularActivityToPathwayAssociation a owl:Class ; rdfs:label "molecular activity to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularActivity ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Pathway ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Association that holds the relationship between a reaction and the pathway it participates in." ; skos:inScheme . @@ -5429,77 +5429,77 @@ biolink:MolecularActivityToPathwayAssociation a owl:Class ; biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a owl:Class ; rdfs:label "named thing associated with likelihood of named thing association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:population_context_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object_context_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; - owl:onProperty biolink:population_context_qualifier ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:population_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], biolink:Association ; skos:inScheme . @@ -5513,14 +5513,14 @@ biolink:NucleicAcidSequenceMotif a owl:Class ; biolink:NucleosomeModification a owl:Class ; rdfs:label "nucleosome modification" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EpigenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneProductIsoformMixin ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenomicEntity ], biolink:BiologicalEntity ; skos:definition "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A." ; skos:inScheme . @@ -5534,76 +5534,76 @@ biolink:ObservedExpectedFrequencyAnalysisResult a owl:Class ; biolink:OrganismTaxonToEnvironmentAssociation a owl:Class ; rdfs:label "organism taxon to environment association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], biolink:Association ; skos:inScheme . biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; rdfs:label "organism taxon to organism taxon interaction" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:associated_environmental_context ], + [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:associated_environmental_context ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:associated_environmental_context ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:associated_environmental_context ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:associated_environmental_context ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:object ], biolink:OrganismTaxonToOrganismTaxonAssociation ; skos:definition "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; skos:inScheme . @@ -5611,31 +5611,31 @@ biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; rdfs:label "organism taxon to organism taxon specialization" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], biolink:OrganismTaxonToOrganismTaxonAssociation ; skos:definition "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; @@ -5644,6 +5644,12 @@ biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; biolink:OrganismToOrganismAssociation a owl:Class ; rdfs:label "organism to organism association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; @@ -5652,12 +5658,6 @@ biolink:OrganismToOrganismAssociation a owl:Class ; [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:IndividualOrganism ; owl:onProperty biolink:object ], @@ -5667,43 +5667,28 @@ biolink:OrganismToOrganismAssociation a owl:Class ; biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "organismal entity as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismalEntity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismalEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:inScheme . biolink:PairwiseMolecularInteraction a owl:Class ; rdfs:label "pairwise molecular interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:interacting_molecules_category ], + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], @@ -5712,25 +5697,40 @@ biolink:PairwiseMolecularInteraction a owl:Class ; owl:onProperty biolink:interacting_molecules_category ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:interacting_molecules_category ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MolecularEntity ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MolecularEntity ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], + owl:maxCardinality 1 ; + owl:onProperty biolink:interacting_molecules_category ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:interacting_molecules_category ], biolink:PairwiseGeneToGeneInteraction ; skos:definition "An interaction at the molecular level between two physical entities" ; skos:inScheme . @@ -5823,19 +5823,19 @@ biolink:PhenotypicFeatureToDiseaseAssociation a owl:Class ; rdfs:label "phenotypic feature to disease association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin ], biolink:Association ; skos:inScheme . @@ -5892,28 +5892,28 @@ biolink:PopulationToPopulationAssociation a owl:Class ; owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between a two populations" ; @@ -5931,194 +5931,194 @@ biolink:PosttranslationalModification a owl:Class ; biolink:PredicateMapping a owl:Class ; rdfs:label "predicate mapping" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:exact_match ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:mapped_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:mapped_predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:mapped_predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:exact_match ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:narrow_match ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:narrow_match ], + owl:maxCardinality 1 ; + owl:onProperty biolink:exact_match ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:exact_match ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:object_derivative_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:mapped_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:exact_match ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_part_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:broad_match ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:exact_match ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:broad_match ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:broad_match ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_derivative_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:mapped_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:broad_match ], [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:broad_match ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:narrow_match ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:broad_match ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], linkml:ClassDefinition ; skos:definition "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; skos:inScheme . @@ -6224,10 +6224,10 @@ biolink:ReactionToCatalystAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], biolink:ReactionToParticipantAssociation ; skos:inScheme . @@ -6236,10 +6236,10 @@ biolink:ReagentTargetedGene a owl:Class ; rdfs:label "reagent targeted gene" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], @@ -6289,23 +6289,23 @@ biolink:SequenceEnum a owl:Class ; biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ; rdfs:label "sequence variant modulates treatment association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:allValuesFrom biolink:Treatment ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; skos:inScheme ; @@ -6317,44 +6317,44 @@ biolink:Serial a owl:Class ; owl:minCardinality 0 ; owl:onProperty biolink:type ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], + owl:minCardinality 0 ; + owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:iso_abbreviation ], + owl:onProperty biolink:volume ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:id ], + owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:volume ], + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:issue ], + owl:minCardinality 0 ; + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:type ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:volume ], + owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:iso_abbreviation ], + owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:issue ], + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:iso_abbreviation ], + owl:onProperty biolink:volume ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:issue ], + owl:maxCardinality 1 ; + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:volume ], + owl:minCardinality 1 ; + owl:onProperty biolink:id ], biolink:Publication ; skos:altLabel "journal" ; skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; @@ -6373,14 +6373,14 @@ biolink:SiRNA a owl:Class ; biolink:SmallMolecule a owl:Class ; rdfs:label "small molecule" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], biolink:MolecularEntity ; skos:altLabel "chemical substance" ; skos:definition "A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion)." ; @@ -6412,15 +6412,15 @@ biolink:Snv a owl:Class ; biolink:SocioeconomicExposure a owl:Class ; rdfs:label "socioeconomic exposure" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ExposureEvent ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; owl:allValuesFrom biolink:SocioeconomicAttribute ; owl:onProperty biolink:has_attribute ], - biolink:Attribute ; + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ExposureEvent ], + biolink:Attribute ; skos:definition "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." ; skos:inScheme . @@ -6471,19 +6471,19 @@ biolink:StudyVariable a owl:Class ; biolink:TaxonToTaxonAssociation a owl:Class ; rdfs:label "taxon to taxon association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; @@ -6507,23 +6507,23 @@ biolink:TextMiningResult a owl:Class ; biolink:TranscriptToGeneRelationship a owl:Class ; rdfs:label "transcript to gene relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Transcript ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Transcript ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:SequenceFeatureRelationship ; skos:definition "A gene is a collection of transcripts" ; skos:inScheme . @@ -6532,16 +6532,16 @@ biolink:TranscriptionFactorBindingSite a owl:Class ; rdfs:label "transcription factor binding site" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:OntologyClass ], biolink:RegulatoryRegion ; skos:altLabel "binding site", "tf binding site" ; @@ -6552,20 +6552,20 @@ biolink:TranscriptionFactorBindingSite a owl:Class ; biolink:VariantAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "variant as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:allValuesFrom biolink:SequenceVariant ; + owl:onProperty biolink:subject ], biolink:VariantToDiseaseAssociation ; skos:inScheme . @@ -6590,79 +6590,79 @@ biolink:VariantToGeneExpressionAssociation a owl:Class ; biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "variant to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], biolink:Association ; skos:inScheme . biolink:VariantToPopulationAssociation a owl:Class ; rdfs:label "variant to population association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_total ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_total ], + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_count ], + owl:onProperty biolink:has_total ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQuantifier ], + owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:FrequencyQuantifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_quotient ], + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:FrequencyQualifierMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], biolink:Association ; skos:definition "An association between a variant and a population, where the variant has particular frequency in the population" ; skos:inScheme . @@ -7236,41 +7236,41 @@ biolink:AdministrativeEntity a owl:Class ; biolink:Article a owl:Class ; rdfs:label "article" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:volume ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:published_in ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; + owl:onProperty biolink:issue ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:issue ], + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:published_in ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:iso_abbreviation ], + owl:onProperty biolink:published_in ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:volume ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:volume ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:published_in ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:iso_abbreviation ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:issue ], biolink:Publication ; skos:definition "a piece of writing on a particular topic presented as a stand-alone section of a larger publication" ; skos:exactMatch fabio:article, @@ -7303,14 +7303,11 @@ biolink:BehavioralFeature a owl:Class ; biolink:BookChapter a owl:Class ; rdfs:label "book chapter" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:published_in ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:chapter ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:chapter ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:published_in ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:volume ], @@ -7320,15 +7317,18 @@ biolink:BookChapter a owl:Class ; [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:volume ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:published_in ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:published_in ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:chapter ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:published_in ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:chapter ], biolink:Publication ; skos:inScheme . @@ -7346,16 +7346,16 @@ biolink:Case a owl:Class ; biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "cell line to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:CellLineToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; @@ -7379,14 +7379,14 @@ biolink:ChemicalEntityToEntityAssociationMixin a owl:Class ; biolink:ChemicalExposure a owl:Class ; rdfs:label "chemical exposure" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_quantitative_value ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ExposureEvent ], [ a owl:Restriction ; owl:allValuesFrom biolink:QuantityValue ; owl:onProperty biolink:has_quantitative_value ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ExposureEvent ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_quantitative_value ], biolink:Attribute ; skos:definition "A chemical exposure is an intake of a particular chemical entity." ; skos:exactMatch ECTO:9000000, @@ -7399,11 +7399,17 @@ biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a owl:C owl:minCardinality 0 ; owl:onProperty biolink:FDA_adverse_event_level ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:FDA_adverse_event_level ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:FDAIDAAdverseEventEnum ; owl:onProperty biolink:FDA_adverse_event_level ], @@ -7411,14 +7417,8 @@ biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a owl:C owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:FDA_adverse_event_level ], biolink:Association ; skos:definition "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect." ; skos:inScheme . @@ -7562,77 +7562,77 @@ biolink:GeneFamily a owl:Class ; biolink:GenomicSequenceLocalization a owl:Class ; rdfs:label "genomic sequence localization" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:end_interbase_coordinate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:start_interbase_coordinate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:genome_build ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:phase ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PhaseEnum ; - owl:onProperty biolink:phase ], [ a owl:Restriction ; owl:allValuesFrom biolink:StrandEnum ; owl:onProperty biolink:strand ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:end_interbase_coordinate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:genome_build ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:StrandEnum ; owl:onProperty biolink:genome_build ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:end_interbase_coordinate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:phase ], [ a owl:Restriction ; owl:allValuesFrom biolink:NucleicAcidEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:start_interbase_coordinate ], + owl:onProperty biolink:phase ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PhaseEnum ; + owl:onProperty biolink:phase ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:strand ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NucleicAcidEntity ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:strand ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:phase ], + owl:onProperty biolink:end_interbase_coordinate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:start_interbase_coordinate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NucleicAcidEntity ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:end_interbase_coordinate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:strand ], + owl:minCardinality 0 ; + owl:onProperty biolink:start_interbase_coordinate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:StrandEnum ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:genome_build ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:SequenceAssociation ; skos:broadMatch dcid:Chromosome ; skos:definition "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; @@ -7642,38 +7642,38 @@ biolink:GenomicSequenceLocalization a owl:Class ; biolink:GenotypeToDiseaseAssociation a owl:Class ; rdfs:label "genotype to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:subject ], biolink:Association ; skos:inScheme ; skos:note "TODO decide no how to model pathogenicity" . @@ -7686,23 +7686,23 @@ biolink:GenotypeToEntityAssociationMixin a owl:Class ; biolink:GeographicLocation a owl:Class ; rdfs:label "geographic location" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; - owl:onProperty biolink:longitude ], - [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:latitude ], + owl:onProperty biolink:longitude ], [ a owl:Restriction ; owl:allValuesFrom xsd:float ; - owl:onProperty biolink:latitude ], + owl:onProperty biolink:longitude ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:longitude ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:float ; owl:onProperty biolink:latitude ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:longitude ], + owl:onProperty biolink:latitude ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:latitude ], biolink:PlanetaryEntity ; skos:definition "a location that can be described in lat/long coordinates" ; skos:exactMatch STY:T083, @@ -7744,13 +7744,13 @@ biolink:OrganismTaxonToEntityAssociation a owl:Class ; biolink:PairwiseGeneToGeneInteraction a owl:Class ; rdfs:label "pairwise gene to gene interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], biolink:GeneToGeneAssociation ; skos:definition "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" ; @@ -7761,10 +7761,10 @@ biolink:Polypeptide a owl:Class ; rdfs:label "polypeptide" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], biolink:BiologicalEntity ; skos:altLabel "amino acid entity" ; skos:definition "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule." ; @@ -7776,41 +7776,41 @@ biolink:Polypeptide a owl:Class ; biolink:ReactionToParticipantAssociation a owl:Class ; rdfs:label "reaction to participant association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:ReactionSideEnum ; owl:onProperty biolink:reaction_side ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ReactionDirectionEnum ; - owl:onProperty biolink:reaction_direction ], + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:stoichiometry ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:reaction_direction ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:reaction_direction ], + owl:onProperty biolink:reaction_side ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:stoichiometry ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ReactionSideEnum ; + owl:maxCardinality 1 ; owl:onProperty biolink:reaction_side ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:ReactionDirectionEnum ; + owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:reaction_side ], + owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:stoichiometry ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; + owl:minCardinality 0 ; owl:onProperty biolink:stoichiometry ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:stoichiometry ], + owl:allValuesFrom biolink:MolecularEntity ; + owl:onProperty biolink:subject ], biolink:ChemicalToChemicalAssociation ; skos:inScheme . @@ -7842,29 +7842,29 @@ biolink:StudyPopulation a owl:Class ; biolink:Treatment a owl:Class ; rdfs:label "treatment" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Procedure ; - owl:onProperty biolink:has_procedure ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Device ; - owl:onProperty biolink:has_device ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_procedure ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_device ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_procedure ], + owl:allValuesFrom biolink:Drug ; + owl:onProperty biolink:has_drug ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_drug ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], + owl:allValuesFrom biolink:Device ; + owl:onProperty biolink:has_device ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Procedure ; + owl:onProperty biolink:has_procedure ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ExposureEvent ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Drug ; - owl:onProperty biolink:has_drug ], biolink:NamedThing ; skos:altLabel "medical action", "medical intervention" ; @@ -7877,38 +7877,38 @@ biolink:Treatment a owl:Class ; biolink:VariantToDiseaseAssociation a owl:Class ; rdfs:label "variant to disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:inScheme ; skos:note "TODO decide no how to model pathogenicity" . @@ -7916,26 +7916,26 @@ biolink:VariantToDiseaseAssociation a owl:Class ; biolink:VariantToGeneAssociation a owl:Class ; rdfs:label "variant to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], biolink:Association ; skos:definition "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" ; skos:inScheme . @@ -8605,23 +8605,23 @@ biolink:ActivityAndBehavior a owl:Class ; biolink:AnatomicalEntityToAnatomicalEntityAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:inScheme . @@ -8653,8 +8653,8 @@ biolink:ChemicalRole a owl:Class ; biolink:ChemicalToChemicalAssociation a owl:Class ; rdfs:label "chemical to chemical association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], @@ -8662,26 +8662,26 @@ biolink:ChemicalToChemicalAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ; skos:inScheme . @@ -8704,7 +8704,6 @@ biolink:Device a owl:Class ; skos:inScheme ; skos:narrowMatch STY:T074, STY:T075, - STY:T122, STY:T203, UMLSSG:DEVI . @@ -8759,56 +8758,56 @@ biolink:FrequencyQualifierMixin a owl:Class ; biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "gene to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], biolink:Association ; skos:inScheme ; skos:narrowMatch WBVocab:Gene-Phenotype-Association, @@ -8864,25 +8863,25 @@ biolink:Onset a owl:Class ; biolink:OrganismTaxonToOrganismTaxonAssociation a owl:Class ; rdfs:label "organism taxon to organism taxon association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:object ], biolink:Association ; skos:definition "A relationship between two organism taxon nodes" ; @@ -8931,10 +8930,10 @@ biolink:RegulatoryRegion a owl:Class ; rdfs:label "regulatory region" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], @@ -9273,10 +9272,10 @@ biolink:CellularComponent a owl:Class ; biolink:DatasetDistribution a owl:Class ; rdfs:label "dataset distribution" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:distribution_download_url ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:distribution_download_url ], [ a owl:Restriction ; owl:minCardinality 0 ; @@ -9289,7 +9288,7 @@ biolink:DatasetDistribution a owl:Class ; biolink:DatasetSummary a owl:Class ; rdfs:label "dataset summary" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:source_logo ], [ a owl:Restriction ; owl:minCardinality 0 ; @@ -9298,14 +9297,14 @@ biolink:DatasetSummary a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:source_web_page ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:source_web_page ], + owl:minCardinality 0 ; + owl:onProperty biolink:source_logo ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:source_logo ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:source_logo ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:source_web_page ], biolink:InformationContentEntity ; skos:definition "an item that holds summary level information about a dataset." ; skos:inScheme . @@ -9336,18 +9335,18 @@ biolink:GeneToGeneAssociation a owl:Class ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], biolink:Association ; skos:altLabel "molecular or genetic interaction" ; @@ -9430,23 +9429,23 @@ biolink:Protein a owl:Class ; biolink:QuantityValue a owl:Class ; rdfs:label "quantity value" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_unit ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_numeric_value ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_numeric_value ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_unit ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty biolink:has_unit ], [ a owl:Restriction ; owl:allValuesFrom xsd:double ; owl:onProperty biolink:has_numeric_value ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_unit ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_numeric_value ], biolink:Annotation ; skos:definition "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" ; skos:inScheme . @@ -9468,15 +9467,15 @@ biolink:SequenceFeatureRelationship a owl:Class ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NucleicAcidEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NucleicAcidEntity ; owl:onProperty biolink:subject ], biolink:Association ; skos:definition "For example, a particular exon is part of a particular transcript or gene" ; @@ -9596,29 +9595,29 @@ biolink:ClinicalAttribute a owl:Class ; biolink:DatasetVersion a owl:Class ; rdfs:label "dataset version" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:Dataset ; owl:onProperty biolink:has_dataset ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:ingest_date ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_distribution ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:has_dataset ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:ingest_date ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Dataset ; - owl:onProperty biolink:has_dataset ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:ingest_date ], + owl:onProperty biolink:has_dataset ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_distribution ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:ingest_date ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_distribution ], [ a owl:Restriction ; owl:allValuesFrom biolink:DatasetDistribution ; owl:onProperty biolink:has_distribution ], @@ -9650,13 +9649,7 @@ biolink:FDAIDAAdverseEventEnum a owl:Class ; biolink:FunctionalAssociation a owl:Class ; rdfs:label "functional association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -9665,8 +9658,14 @@ biolink:FunctionalAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." ; skos:inScheme . @@ -10047,38 +10046,38 @@ biolink:CellularOrganism a owl:Class ; biolink:ChemicalMixture a owl:Class ; rdfs:label "chemical mixture" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:is_supplement ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:highest_FDA_approval_status ], - [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:highest_FDA_approval_status ], + owl:onProperty biolink:drug_regulatory_status_world_wide ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:highest_FDA_approval_status ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:is_supplement ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:DrugDeliveryEnum ; owl:onProperty biolink:routes_of_delivery ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:drug_regulatory_status_world_wide ], + owl:onProperty biolink:highest_FDA_approval_status ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:is_supplement ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DrugDeliveryEnum ; - owl:onProperty biolink:routes_of_delivery ], + owl:minCardinality 0 ; + owl:onProperty biolink:is_supplement ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:drug_regulatory_status_world_wide ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:routes_of_delivery ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:is_supplement ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:drug_regulatory_status_world_wide ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:highest_FDA_approval_status ], biolink:ChemicalEntity ; skos:closeMatch dcid:ChemicalCompound ; skos:definition "A chemical mixture is a chemical entity composed of two or more molecular entities." ; @@ -10104,29 +10103,29 @@ biolink:GeneProductMixin a owl:Class ; biolink:GeneToDiseaseAssociation a owl:Class ; rdfs:label "gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; skos:closeMatch dcid:DiseaseGeneAssociation ; skos:exactMatch SIO:000983 ; @@ -10143,15 +10142,24 @@ biolink:MolecularActivity a owl:Class ; rdfs:label "molecular activity" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:enabled_by ], + owl:onProperty biolink:has_output ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:Occurrent ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_input ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:has_output ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:enabled_by ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; @@ -10160,20 +10168,11 @@ biolink:MolecularActivity a owl:Class ; owl:minCardinality 0 ; owl:onProperty biolink:has_output ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:has_output ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:has_input ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; - owl:onProperty biolink:enabled_by ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_input ], biolink:BiologicalProcessOrActivity ; skos:altLabel "molecular event", "molecular function", @@ -10193,37 +10192,37 @@ biolink:PhysicalEssenceOrOccurrent a owl:Class ; biolink:RetrievalSource a owl:Class ; rdfs:label "retrieval source" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:resource_role ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:resource_id ], + owl:onProperty biolink:resource_role ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:minCardinality 0 ; owl:onProperty biolink:upstream_resource_ids ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:xref ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ResourceRoleEnum ; - owl:onProperty biolink:resource_role ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:resource_id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:upstream_resource_ids ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:resource_id ], + owl:onProperty biolink:upstream_resource_ids ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ResourceRoleEnum ; + owl:onProperty biolink:resource_role ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:resource_id ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], + owl:minCardinality 1 ; + owl:onProperty biolink:resource_role ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:resource_role ], + owl:onProperty biolink:resource_id ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:upstream_resource_ids ], biolink:InformationContentEntity ; skos:definition "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; @@ -10568,10 +10567,10 @@ biolink:Drug a owl:Class ; rdfs:label "drug" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], + owl:someValuesFrom biolink:OntologyClass ], biolink:MolecularMixture ; skos:broadMatch STY:T121 ; skos:definition "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease" ; @@ -10594,23 +10593,23 @@ biolink:EntityToPhenotypicFeatureAssociationMixin a owl:Class ; biolink:Genotype a owl:Class ; rdfs:label "genotype" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_zygosity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_zygosity ], [ a owl:Restriction ; owl:allValuesFrom biolink:Zygosity ; owl:onProperty biolink:has_zygosity ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_zygosity ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenomicEntity ], biolink:BiologicalEntity ; skos:definition "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background" ; skos:exactMatch , @@ -10712,68 +10711,68 @@ biolink:AgentTypeEnum a owl:Class ; biolink:Entity a owl:Class ; rdfs:label "entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:deprecated ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Attribute ; + owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:description ], + owl:onProperty biolink:deprecated ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:narrative_text ; owl:onProperty biolink:description ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:type ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:label_type ; owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:deprecated ], + owl:maxCardinality 1 ; + owl:onProperty biolink:iri ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:iri ], + owl:onProperty biolink:type ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Attribute ; + owl:minCardinality 0 ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; - owl:allValuesFrom biolink:narrative_text ; + owl:minCardinality 0 ; + owl:onProperty biolink:description ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:description ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:category ], + owl:onProperty biolink:deprecated ], [ a owl:Restriction ; - owl:allValuesFrom biolink:iri_type ; + owl:minCardinality 0 ; owl:onProperty biolink:iri ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; - owl:onProperty biolink:deprecated ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:iri_type ; owl:onProperty biolink:iri ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:type ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_attribute ], + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:category ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:category ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:boolean ; + owl:onProperty biolink:deprecated ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:label_type ; + owl:onProperty biolink:name ], linkml:ClassDefinition ; skos:definition "Root Biolink Model class for all things and informational relationships, real or imagined." ; skos:inScheme . @@ -10871,13 +10870,13 @@ biolink:label_type a rdfs:Datatype ; biolink:OrganismalEntity a owl:Class ; rdfs:label "organismal entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SubjectOfInvestigation ], - [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:SubjectOfInvestigation ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:has_attribute ], biolink:BiologicalEntity ; skos:definition "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities" ; @@ -10978,17 +10977,11 @@ biolink:GeneOrGeneProductOrChemicalPartQualifierEnum a owl:Class ; biolink:BiologicalProcessOrActivity a owl:Class ; rdfs:label "biological process or activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:PhysicalEntity ; - owl:onProperty biolink:enabled_by ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_input ], + owl:onProperty biolink:has_output ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:enabled_by ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Occurrent ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:enabled_by ], @@ -10996,19 +10989,25 @@ biolink:BiologicalProcessOrActivity a owl:Class ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:has_output ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_output ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:minCardinality 0 ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_output ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:Occurrent ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PhysicalEntity ; + owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_output ], + owl:onProperty biolink:has_input ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:has_input ], biolink:BiologicalEntity ; skos:definition "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system." ; @@ -11017,38 +11016,38 @@ biolink:BiologicalProcessOrActivity a owl:Class ; biolink:Agent a owl:Class ; rdfs:label "agent" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:address ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:affiliation ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], + owl:minCardinality 0 ; + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:address ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:affiliation ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:affiliation ], + owl:onProperty biolink:address ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:name ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], + owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:address ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:name ], biolink:AdministrativeEntity ; skos:altLabel "group" ; skos:definition "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; @@ -11167,13 +11166,13 @@ biolink:BiologicalProcess a owl:Class ; biolink:MolecularEntity a owl:Class ; rdfs:label "molecular entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:boolean ; owl:onProperty biolink:is_metabolite ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:is_metabolite ], [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; + owl:minCardinality 0 ; owl:onProperty biolink:is_metabolite ], biolink:ChemicalEntity ; skos:definition "A molecular entity is a chemical entity composed of individual or covalently bonded atoms." ; @@ -11186,14 +11185,14 @@ biolink:MolecularEntity a owl:Class ; biolink:OrganismTaxon a owl:Class ; rdfs:label "organism taxon" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_taxonomic_rank ], - [ a owl:Restriction ; owl:allValuesFrom biolink:TaxonomicRank ; owl:onProperty biolink:has_taxonomic_rank ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_taxonomic_rank ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_taxonomic_rank ], biolink:NamedThing ; skos:altLabel "taxon", "taxonomic classification" ; @@ -11207,41 +11206,41 @@ biolink:OrganismTaxon a owl:Class ; biolink:InformationContentEntity a owl:Class ; rdfs:label "information content entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:format ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:date ; - owl:onProperty biolink:creation_date ], + owl:maxCardinality 1 ; + owl:onProperty biolink:rights ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:license ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:rights ], + owl:minCardinality 0 ; + owl:onProperty biolink:format ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:creation_date ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:format ], + owl:onProperty biolink:license ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:rights ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:date ; + owl:onProperty biolink:creation_date ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:license ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:format ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:rights ], + owl:onProperty biolink:creation_date ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:format ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:creation_date ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:license ], + owl:onProperty biolink:rights ], biolink:NamedThing ; skos:altLabel "information", "information artefact", @@ -11300,50 +11299,50 @@ biolink:CausalMechanismQualifierEnum a owl:Class ; biolink:Attribute a owl:Class ; rdfs:label "attribute" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_attribute_type ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_qualitative_value ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:iri_type ; - owl:onProperty biolink:iri ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], - [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_qualitative_value ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_quantitative_value ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:has_qualitative_value ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_qualitative_value ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:name ], + owl:allValuesFrom biolink:QuantityValue ; + owl:onProperty biolink:has_quantitative_value ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:iri ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:name ], + owl:onProperty biolink:iri ], [ a owl:Restriction ; owl:allValuesFrom biolink:label_type ; owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:allValuesFrom biolink:QuantityValue ; - owl:onProperty biolink:has_quantitative_value ], + owl:allValuesFrom biolink:iri_type ; + owl:onProperty biolink:iri ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; + owl:minCardinality 0 ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:iri ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_quantitative_value ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass ], biolink:NamedThing ; skos:definition "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; skos:exactMatch SIO:000614 ; @@ -11355,35 +11354,35 @@ biolink:predicate_type a rdfs:Datatype ; biolink:Gene a owl:Class ; rdfs:label "gene" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenomicEntity ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:symbol ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneOrGeneProduct ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:symbol ], + owl:minCardinality 0 ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:symbol ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:symbol ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:GeneOrGeneProduct ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:xref ], + owl:maxCardinality 1 ; + owl:onProperty biolink:symbol ], biolink:BiologicalEntity ; skos:broadMatch ; skos:definition "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions." ; @@ -11397,23 +11396,14 @@ biolink:Gene a owl:Class ; biolink:SequenceVariant a owl:Class ; rdfs:label "sequence variant" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:id ], + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:has_gene ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_biological_sequence ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_gene ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], @@ -11421,14 +11411,23 @@ biolink:SequenceVariant a owl:Class ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:has_gene ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_gene ], + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenomicEntity ], biolink:BiologicalEntity ; skos:altLabel "allele" ; skos:closeMatch , @@ -11472,68 +11471,68 @@ biolink:AnatomicalEntity a owl:Class ; biolink:Publication a owl:Class ; rdfs:label "publication" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:authors ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:keywords ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:mesh_terms ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:summary ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:mesh_terms ], + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:keywords ], + owl:onProperty biolink:pages ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], + owl:minCardinality 0 ; + owl:onProperty biolink:pages ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:publication_type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:pages ], + owl:onProperty biolink:authors ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:xref ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:publication_type ], + owl:minCardinality 0 ; + owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Agent ; - owl:onProperty biolink:authors ], + owl:maxCardinality 1 ; + owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:mesh_terms ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Agent ; + owl:onProperty biolink:authors ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:keywords ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:summary ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:keywords ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:summary ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:pages ], + owl:minCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:publication_type ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], biolink:InformationContentEntity ; skos:definition "Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP)." ; skos:exactMatch IAO:0000311 ; @@ -11567,55 +11566,55 @@ biolink:ChemicalEntity a owl:Class ; rdfs:label "chemical entity" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:max_tolerated_dose ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:onProperty biolink:trade_name ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], + owl:maxCardinality 1 ; + owl:onProperty biolink:max_tolerated_dose ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:maxCardinality 1 ; + owl:onProperty biolink:is_toxic ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:max_tolerated_dose ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:max_tolerated_dose ], [ a owl:Restriction ; owl:allValuesFrom xsd:boolean ; owl:onProperty biolink:is_toxic ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalRole ; - owl:onProperty biolink:has_chemical_role ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:available_from ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; owl:onProperty biolink:trade_name ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:is_toxic ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:trade_name ], + owl:onProperty biolink:max_tolerated_dose ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:trade_name ], + owl:allValuesFrom biolink:ChemicalRole ; + owl:onProperty biolink:has_chemical_role ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:allValuesFrom biolink:DrugAvailabilityEnum ; owl:onProperty biolink:available_from ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:is_toxic ], + owl:onProperty biolink:has_chemical_role ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_chemical_role ], + owl:onProperty biolink:available_from ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:trade_name ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence ], biolink:NamedThing ; skos:broadMatch STY:T167 ; skos:definition "A chemical entity is a physical entity that pertains to chemistry or biochemistry." ; @@ -11750,254 +11749,254 @@ biolink:association_slot a owl:DatatypeProperty ; biolink:Association a owl:Class ; rdfs:label "association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Publication ; - owl:onProperty biolink:publications ], - [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:adjusted_p_value ], + owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object_category_closure ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:time_type ; - owl:onProperty biolink:timepoint ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:subject_namespace ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:agent_type ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AgentTypeEnum ; - owl:onProperty biolink:agent_type ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:type ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_closure ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_namespace ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:subject_category_closure ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:knowledge_level ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:primary_knowledge_source ], + owl:onProperty biolink:subject_label_closure ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_closure ], + owl:onProperty biolink:adjusted_p_value ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:timepoint ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_category ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:knowledge_level ], + owl:allValuesFrom biolink:Publication ; + owl:onProperty biolink:publications ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:adjusted_p_value ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object_category ], + owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:original_object ], + owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:knowledge_source ], + owl:onProperty biolink:subject_closure ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:negated ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:original_subject ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_category_closure ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:agent_type ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_namespace ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_category ], + owl:onProperty biolink:qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_category ], + owl:onProperty biolink:agent_type ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualifiers ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_label_closure ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:negated ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:KnowledgeLevelEnum ; - owl:onProperty biolink:knowledge_level ], + owl:onProperty biolink:publications ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject_namespace ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:p_value ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_label_closure ], + owl:onProperty biolink:qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_closure ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_label_closure ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_namespace ], + owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:timepoint ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:knowledge_source ], + owl:onProperty biolink:subject_category ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:category ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:original_subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:p_value ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:original_predicate ], + owl:onProperty biolink:qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:category ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:original_subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:EvidenceType ; owl:onProperty biolink:has_evidence ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_category ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:aggregator_knowledge_source ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_namespace ], + owl:onProperty biolink:aggregator_knowledge_source ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_evidence ], + owl:onProperty biolink:subject_category_closure ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:type ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_closure ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_category ], + owl:allValuesFrom xsd:float ; + owl:onProperty biolink:p_value ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:original_subject ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:subject_category ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:aggregator_knowledge_source ], + owl:onProperty biolink:object_closure ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:original_object ], + owl:minCardinality 1 ; + owl:onProperty biolink:knowledge_level ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_label_closure ], + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:agent_type ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:qualifiers ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualifier ], + owl:onProperty biolink:original_object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:p_value ], + owl:onProperty biolink:adjusted_p_value ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:knowledge_source ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:subject_category_closure ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_category ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:category ], + owl:onProperty biolink:retrieval_source_ids ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:retrieval_source_ids ], + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:p_value ], + owl:allValuesFrom biolink:AgentTypeEnum ; + owl:onProperty biolink:agent_type ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:qualifiers ], + owl:onProperty biolink:object_category_closure ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:original_object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:knowledge_source ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:allValuesFrom xsd:boolean ; + owl:onProperty biolink:negated ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_category_closure ], + owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; - owl:allValuesFrom biolink:RetrievalSource ; - owl:onProperty biolink:retrieval_source_ids ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_category ], [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; - owl:onProperty biolink:negated ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; - owl:onProperty biolink:adjusted_p_value ], + owl:allValuesFrom biolink:KnowledgeLevelEnum ; + owl:onProperty biolink:knowledge_level ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:negated ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:original_subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:publications ], + owl:maxCardinality 1 ; + owl:onProperty biolink:knowledge_source ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:negated ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:object_label_closure ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_label_closure ], + owl:onProperty biolink:object_closure ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:knowledge_source ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:time_type ; + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:aggregator_knowledge_source ], + owl:onProperty biolink:original_object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:timepoint ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:knowledge_level ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:subject_category ], + owl:onProperty biolink:object_category ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:primary_knowledge_source ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_namespace ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:float ; - owl:onProperty biolink:p_value ], + owl:onProperty biolink:adjusted_p_value ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:RetrievalSource ; + owl:onProperty biolink:retrieval_source_ids ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualifier ], + owl:onProperty biolink:type ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:original_object ], biolink:Entity ; skos:definition "A typed association between two entities, supported by evidence" ; skos:exactMatch OBAN:association, @@ -12017,38 +12016,38 @@ biolink:related_to_at_instance_level a owl:DatatypeProperty, biolink:NamedThing a owl:Class ; rdfs:label "named thing" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:category ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:provided_by ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:label_type ; + owl:onProperty biolink:full_name ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:provided_by ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:category ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:full_name ], + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:allValuesFrom biolink:label_type ; - owl:onProperty biolink:full_name ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:synonym ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:category ], + owl:minCardinality 0 ; + owl:onProperty biolink:full_name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:xref ], + owl:onProperty biolink:synonym ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:full_name ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:label_type ; - owl:onProperty biolink:synonym ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:provided_by ], + owl:onProperty biolink:category ], biolink:Entity ; skos:definition "a databased entity or concept/class" ; skos:exactMatch STY:T071, @@ -12100,183 +12099,210 @@ biolink:subject a owl:ObjectProperty ; skos:inScheme . [] a owl:Restriction ; - rdfs:subClassOf biolink:StudyVariable ; + rdfs:subClassOf biolink:MolecularMixture ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyVariable . + owl:someValuesFrom biolink:MolecularMixture . [] a owl:Restriction ; - rdfs:subClassOf biolink:EntityToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:ChemicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:ChemicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugToGeneInteractionExposure ; + rdfs:subClassOf biolink:MicroRNA ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugToGeneInteractionExposure . + owl:someValuesFrom biolink:MicroRNA . [] a owl:Restriction ; - rdfs:subClassOf biolink:LogOddsAnalysisResult ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:LogOddsAnalysisResult . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeature . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:NucleicAcidEntity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:NucleicAcidEntity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneToDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneToDiseaseAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ClinicalAttribute ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ClinicalAttribute . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Polypeptide ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Polypeptide . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeographicLocationAtTime ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeographicLocationAtTime . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ReactionToParticipantAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ReactionToParticipantAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:predicate_type ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ] ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PathologicalEntityMixin . + rdfs:subClassOf biolink:SequenceVariantModulatesTreatmentAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:SequenceVariantModulatesTreatmentAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Exon ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Exon . [] a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SpecificityQuantifier . + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismToOrganismAssociation ; + rdfs:subClassOf biolink:EntityToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismToOrganismAssociation . + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:RNAProduct ; + rdfs:subClassOf biolink:MolecularEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RNAProduct . + owl:someValuesFrom biolink:MolecularEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:StudyPopulation ; + rdfs:subClassOf biolink:Study ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyPopulation . + owl:someValuesFrom biolink:Study . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToGeneAssociation ; + rdfs:subClassOf biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToGeneAssociation . + owl:someValuesFrom biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellLine ; + rdfs:subClassOf biolink:Haplotype ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLine . + owl:someValuesFrom biolink:Haplotype . [] a owl:Restriction ; - rdfs:subClassOf biolink:ContributorAssociation ; + rdfs:subClassOf biolink:VariantToGeneExpressionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ContributorAssociation . + owl:someValuesFrom biolink:VariantToGeneExpressionAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Protein ; + rdfs:subClassOf biolink:WebPage ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Protein . + owl:someValuesFrom biolink:WebPage . [] a owl:Restriction ; - rdfs:subClassOf biolink:InformationContentEntityToNamedThingAssociation ; + rdfs:subClassOf biolink:Dataset ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:InformationContentEntityToNamedThingAssociation . + owl:someValuesFrom biolink:Dataset . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SensitivityQuantifier . + rdfs:subClassOf biolink:Vertebrate ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Vertebrate . [] a owl:Restriction ; - rdfs:subClassOf biolink:PairwiseGeneToGeneInteraction ; + rdfs:subClassOf biolink:GeneToGeneHomologyAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PairwiseGeneToGeneInteraction . + owl:someValuesFrom biolink:GeneToGeneHomologyAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ExonToTranscriptRelationship ; + rdfs:subClassOf biolink:FoodAdditive ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExonToTranscriptRelationship . + owl:someValuesFrom biolink:FoodAdditive . [] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSampleDerivationAssociation ; + rdfs:subClassOf biolink:Patent ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSampleDerivationAssociation . + owl:someValuesFrom biolink:Patent . [] a owl:Restriction ; - rdfs:subClassOf biolink:StudyResult ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyResult . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneAffectsChemicalAssociation ; + rdfs:subClassOf biolink:SiRNA ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneAffectsChemicalAssociation . + owl:someValuesFrom biolink:SiRNA . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonAssociation ; + rdfs:subClassOf biolink:InformationContentEntityToNamedThingAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonAssociation . + owl:someValuesFrom biolink:InformationContentEntityToNamedThingAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityAssociation ; + rdfs:subClassOf biolink:PhenotypicSex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityAssociation . + owl:someValuesFrom biolink:PhenotypicSex . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToExpressionSiteAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToExpressionSiteAssociation . + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin . [] a owl:Restriction ; rdfs:subClassOf biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation ; @@ -12284,57 +12310,96 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Polypeptide ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Polypeptide . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Serial ; + rdfs:subClassOf biolink:CorrelatedGeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Serial . + owl:someValuesFrom biolink:CorrelatedGeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismalEntity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismalEntity . + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhysicalEntity ; + rdfs:subClassOf biolink:Association ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhysicalEntity . + owl:someValuesFrom biolink:Association . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicExposure ; + rdfs:subClassOf biolink:GenotypeToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicExposure . + owl:someValuesFrom biolink:GenotypeToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:InformationContentEntity ; + rdfs:subClassOf biolink:SocioeconomicExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:InformationContentEntity . + owl:someValuesFrom biolink:SocioeconomicExposure . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ExposureEvent ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:timepoint ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:timepoint ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:time_type ; - owl:onProperty biolink:timepoint ] ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ExposureEvent . + owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonSpecialization ; + rdfs:subClassOf biolink:DiagnosticAid ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonSpecialization . + owl:someValuesFrom biolink:DiagnosticAid . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], @@ -12342,461 +12407,587 @@ biolink:subject a owl:ObjectProperty ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:predicate_type ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; - owl:onProperty biolink:subject ] ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin . + owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:SmallMolecule ; + rdfs:subClassOf biolink:GeneToGeneFamilyAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SmallMolecule . + owl:someValuesFrom biolink:GeneToGeneFamilyAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ObservedExpectedFrequencyAnalysisResult ; + rdfs:subClassOf biolink:GenomicBackgroundExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ObservedExpectedFrequencyAnalysisResult . + owl:someValuesFrom biolink:GenomicBackgroundExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:Activity ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:SpecificityQuantifier . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:AccessibleDnaRegion ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Activity . + owl:someValuesFrom biolink:AccessibleDnaRegion . [] a owl:Restriction ; - rdfs:subClassOf biolink:Disease ; + rdfs:subClassOf biolink:ChiSquaredAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Disease . + owl:someValuesFrom biolink:ChiSquaredAnalysisResult . [] a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct . + owl:someValuesFrom biolink:PhysicalEssence . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicFeature ; + rdfs:subClassOf biolink:PhysicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicFeature . + owl:someValuesFrom biolink:PhysicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:CommonDataElement ; + rdfs:subClassOf biolink:ClinicalModifier ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CommonDataElement . + owl:someValuesFrom biolink:ClinicalModifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToPopulationAssociation ; + rdfs:subClassOf biolink:Entity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToPopulationAssociation . + owl:someValuesFrom biolink:Entity . [] a owl:Restriction ; - rdfs:subClassOf biolink:Onset ; + rdfs:subClassOf biolink:PhenotypicFeatureToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Onset . + owl:someValuesFrom biolink:PhenotypicFeatureToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:AccessibleDnaRegion ; + rdfs:subClassOf biolink:Article ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AccessibleDnaRegion . + owl:someValuesFrom biolink:Article . [] a owl:Restriction ; - rdfs:subClassOf biolink:Food ; + rdfs:subClassOf biolink:DiseaseToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Food . + owl:someValuesFrom biolink:DiseaseToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Snv ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:MaterialSample ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:BehavioralExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Snv . + owl:someValuesFrom biolink:BehavioralExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceFeatureRelationship ; + rdfs:subClassOf biolink:OrganismAttribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceFeatureRelationship . + owl:someValuesFrom biolink:OrganismAttribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularMixture ; + rdfs:subClassOf biolink:ComplexChemicalExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularMixture . + owl:someValuesFrom biolink:ComplexChemicalExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseToExposureEventAssociation ; + rdfs:subClassOf biolink:CellularOrganism ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseToExposureEventAssociation . + owl:someValuesFrom biolink:CellularOrganism . [] a owl:Restriction ; - rdfs:subClassOf biolink:PlanetaryEntity ; + rdfs:subClassOf biolink:AnatomicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PlanetaryEntity . + owl:someValuesFrom biolink:AnatomicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneHomologyAssociation ; + rdfs:subClassOf biolink:ContributorAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneHomologyAssociation . + owl:someValuesFrom biolink:ContributorAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalGeneInteractionAssociation ; + rdfs:subClassOf biolink:SmallMolecule ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalGeneInteractionAssociation . + owl:someValuesFrom biolink:SmallMolecule . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Hospitalization ; + rdfs:subClassOf biolink:InformationContentEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Hospitalization . + owl:someValuesFrom biolink:InformationContentEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneHasVariantThatContributesToDiseaseAssociation ; + rdfs:subClassOf biolink:RelativeFrequencyAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneHasVariantThatContributesToDiseaseAssociation . + owl:someValuesFrom biolink:RelativeFrequencyAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalMixture ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalMixture . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:Occurrent . [] a owl:Restriction ; - rdfs:subClassOf biolink:CaseToPhenotypicFeatureAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CaseToPhenotypicFeatureAssociation . + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_percentage ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:has_total ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_total ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:double ; + owl:onProperty biolink:has_percentage ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_total ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:double ; + owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_percentage ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:FrequencyQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToPathwayAssociation ; + rdfs:subClassOf biolink:DrugToGeneInteractionExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToPathwayAssociation . + owl:someValuesFrom biolink:DrugToGeneInteractionExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:Gene ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Gene . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneOrGeneProduct . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:OrganismTaxonToEnvironmentAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:OrganismTaxonToEnvironmentAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:NamedThing ; + rdfs:subClassOf biolink:GeneFamily ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NamedThing . + owl:someValuesFrom biolink:GeneFamily . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin . + rdfs:subClassOf biolink:Zygosity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Zygosity . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneticInheritance ; + rdfs:subClassOf biolink:DatasetVersion ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneticInheritance . + owl:someValuesFrom biolink:DatasetVersion . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhysiologicalProcess ; + rdfs:subClassOf biolink:ChemicalGeneInteractionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhysiologicalProcess . + owl:someValuesFrom biolink:ChemicalGeneInteractionAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Virus ; + rdfs:subClassOf biolink:EnvironmentalExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Virus . + owl:someValuesFrom biolink:EnvironmentalExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToLocationAssociation ; + rdfs:subClassOf biolink:PathologicalAnatomicalStructure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . + owl:someValuesFrom biolink:PathologicalAnatomicalStructure . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToMolecularActivityAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToMolecularActivityAssociation . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:SensitivityQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:Fungus ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonInteraction ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Fungus . + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonInteraction . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneProductRelationship ; + rdfs:subClassOf biolink:CodingSequence ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneProductRelationship . + owl:someValuesFrom biolink:CodingSequence . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:Pathway ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:Pathway . [] a owl:Restriction ; - rdfs:subClassOf biolink:PairwiseMolecularInteraction ; + rdfs:subClassOf biolink:BiologicalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PairwiseMolecularInteraction . + owl:someValuesFrom biolink:BiologicalProcess . [] a owl:Restriction ; - rdfs:subClassOf biolink:Genome ; + rdfs:subClassOf biolink:SequenceAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Genome . + owl:someValuesFrom biolink:SequenceAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Pathway ; + rdfs:subClassOf biolink:ChemicalAffectsGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Pathway . + owl:someValuesFrom biolink:ChemicalAffectsGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetDistribution ; + rdfs:subClassOf biolink:ExposureEventToOutcomeAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetDistribution . + owl:someValuesFrom biolink:ExposureEventToOutcomeAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ComplexChemicalExposure ; + rdfs:subClassOf biolink:GenotypeToVariantAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ComplexChemicalExposure . + owl:someValuesFrom biolink:GenotypeToVariantAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:GenotypeToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:GenotypeToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:BehavioralFeature ; + rdfs:subClassOf biolink:GeneToGoTermAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehavioralFeature . + owl:someValuesFrom biolink:GeneToGoTermAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:RelativeFrequencyAnalysisResult ; + rdfs:subClassOf biolink:ClinicalMeasurement ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RelativeFrequencyAnalysisResult . + owl:someValuesFrom biolink:ClinicalMeasurement . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Outcome ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:predicate_type ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ] ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin . + owl:someValuesFrom biolink:GeneToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:BookChapter ; + rdfs:subClassOf biolink:Procedure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BookChapter . + owl:someValuesFrom biolink:Procedure . [] a owl:Restriction ; - rdfs:subClassOf biolink:CodingSequence ; + rdfs:subClassOf biolink:DrugToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CodingSequence . + owl:someValuesFrom biolink:DrugToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation ; + rdfs:subClassOf biolink:LifeStage ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . + owl:someValuesFrom biolink:LifeStage . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass . + rdfs:subClassOf biolink:ClinicalFinding ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ClinicalFinding . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin . + rdfs:subClassOf biolink:RNAProductIsoform ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:RNAProductIsoform . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:symbol_type ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:name ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineMixin . + rdfs:subClassOf biolink:Protein ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Protein . [] a owl:Restriction ; - rdfs:subClassOf biolink:Entity ; + rdfs:subClassOf biolink:FunctionalAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Entity . + owl:someValuesFrom biolink:FunctionalAssociation . [] a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:SubjectOfInvestigation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneCoexpressionAssociation ; + rdfs:subClassOf biolink:OrganismalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneCoexpressionAssociation . + owl:someValuesFrom biolink:OrganismalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:LifeStage ; + rdfs:subClassOf biolink:RegulatoryRegion ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:LifeStage . + owl:someValuesFrom biolink:RegulatoryRegion . [] a owl:Restriction ; - rdfs:subClassOf biolink:Dataset ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:biological_sequence ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_biological_sequence ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EpigenomicEntity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GenotypeToGenotypePartAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Dataset . + owl:someValuesFrom biolink:GenotypeToGenotypePartAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:SequenceFeatureRelationship ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:SequenceFeatureRelationship . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ProteinDomain ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ProteinDomain . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ChemicalToChemicalDerivationAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ChemicalToChemicalDerivationAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:VariantToGeneAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:VariantToGeneAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:JournalArticle ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:JournalArticle . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ProcessedMaterial ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ProcessedMaterial . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ExposureEventToPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ExposureEventToPhenotypicFeatureAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:BiologicalProcessOrActivity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:BiologicalProcessOrActivity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:VariantToPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:VariantToPhenotypicFeatureAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PathologicalAnatomicalExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PathologicalAnatomicalExposure . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation . + owl:someValuesFrom biolink:FeatureOrDiseaseQualifiersToEntityMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Human ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:time_type ; + owl:onProperty biolink:timepoint ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:timepoint ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:timepoint ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ExposureEvent . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:CellLine ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Human . + owl:someValuesFrom biolink:CellLine . [] a owl:Restriction ; - rdfs:subClassOf biolink:ExposureEventToOutcomeAssociation ; + rdfs:subClassOf biolink:GeneToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExposureEventToOutcomeAssociation . + owl:someValuesFrom biolink:GeneToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:TaxonToTaxonAssociation ; + rdfs:subClassOf biolink:StudyVariable ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TaxonToTaxonAssociation . + owl:someValuesFrom biolink:StudyVariable . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PathognomonicityQuantifier . + rdfs:subClassOf biolink:EvidenceType ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:EvidenceType . [] a owl:Restriction ; - rdfs:subClassOf biolink:Case ; + rdfs:subClassOf biolink:Event ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Case . + owl:someValuesFrom biolink:Event . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToCellularComponentAssociation ; + rdfs:subClassOf biolink:Treatment ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToCellularComponentAssociation . + owl:someValuesFrom biolink:Treatment . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:allValuesFrom ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MaterialSample ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], @@ -12804,306 +12995,255 @@ biolink:subject a owl:ObjectProperty ; owl:allValuesFrom biolink:predicate_type ; owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin . + owl:someValuesFrom biolink:FrequencyQualifierMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToPhenotypicFeatureAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToPhenotypicFeatureAssociation . + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_gene_or_gene_product ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:has_gene_or_gene_product ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneGroupingMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Plant ; + rdfs:subClassOf biolink:DruggableGeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Plant . + owl:someValuesFrom biolink:DruggableGeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Vertebrate ; + rdfs:subClassOf biolink:Attribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Vertebrate . + owl:someValuesFrom biolink:Attribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToGeneExpressionAssociation ; + rdfs:subClassOf biolink:Activity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToGeneExpressionAssociation . + owl:someValuesFrom biolink:Activity . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypicSex ; + rdfs:subClassOf biolink:ClinicalIntervention ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypicSex . + owl:someValuesFrom biolink:ClinicalIntervention . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChiSquaredAnalysisResult ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChiSquaredAnalysisResult . + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:symbol_type ; + owl:onProperty biolink:name ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MacromolecularMachineMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenomicSequenceLocalization ; + rdfs:subClassOf biolink:PhysiologicalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenomicSequenceLocalization . + owl:someValuesFrom biolink:PhysiologicalProcess . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Outcome . + rdfs:subClassOf biolink:GeneticInheritance ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneticInheritance . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntityAssessesNamedThingAssociation ; + rdfs:subClassOf biolink:Hospitalization ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntityAssessesNamedThingAssociation . + owl:someValuesFrom biolink:Hospitalization . [] a owl:Restriction ; - rdfs:subClassOf biolink:CausalGeneToDiseaseAssociation ; + rdfs:subClassOf biolink:CaseToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CausalGeneToDiseaseAssociation . + owl:someValuesFrom biolink:CaseToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismAttribute ; + rdfs:subClassOf biolink:CellularComponent ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismAttribute . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:DrugExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugExposure . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalModifier ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalModifier . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToGenotypePartAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToGenotypePartAssociation . + owl:someValuesFrom biolink:CellularComponent . [] a owl:Restriction ; - rdfs:subClassOf biolink:Attribute ; + rdfs:subClassOf biolink:SequenceVariant ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Attribute . + owl:someValuesFrom biolink:SequenceVariant . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinIsoform ; + rdfs:subClassOf biolink:PairwiseGeneToGeneInteraction ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinIsoform . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneProductIsoformMixin . + owl:someValuesFrom biolink:PairwiseGeneToGeneInteraction . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinFamily ; + rdfs:subClassOf biolink:Behavior ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinFamily . + owl:someValuesFrom biolink:Behavior . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_percentage ], + owl:onProperty biolink:phenotypic_state ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_quotient ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:expression_site ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_count ], + owl:onProperty biolink:phenotypic_state ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:has_count ], + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_percentage ], + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_total ], + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_count ], + owl:onProperty biolink:stage_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:expression_site ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_quotient ], + owl:onProperty biolink:expression_site ], [ a owl:Restriction ; - owl:allValuesFrom xsd:double ; - owl:onProperty biolink:has_quotient ], + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:phenotypic_state ], [ a owl:Restriction ; - owl:allValuesFrom xsd:double ; - owl:onProperty biolink:has_percentage ] ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQuantifier . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetVersion ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetVersion . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ReagentTargetedGene ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReagentTargetedGene . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ProcessedMaterial ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProcessedMaterial . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToDiseaseAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToDiseaseAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToPathwayAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToPathwayAssociation . + owl:someValuesFrom biolink:GeneExpressionMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:CorrelatedGeneToDiseaseAssociation ; + rdfs:subClassOf biolink:Publication ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CorrelatedGeneToDiseaseAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:CellLine ; - owl:onProperty biolink:subject ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CellLineToEntityAssociationMixin . + owl:someValuesFrom biolink:Publication . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalFoodContaminant ; + rdfs:subClassOf biolink:PairwiseMolecularInteraction ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalFoodContaminant . + owl:someValuesFrom biolink:PairwiseMolecularInteraction . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalTrial ; + rdfs:subClassOf biolink:BioticExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalTrial . + owl:someValuesFrom biolink:BioticExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:ExposureEventToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:Case ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExposureEventToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:Case . [] a owl:Restriction ; - rdfs:subClassOf biolink:Book ; + rdfs:subClassOf biolink:LogOddsAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Book . + owl:someValuesFrom biolink:LogOddsAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellLineAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:IndividualOrganism ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLineAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:IndividualOrganism . [] a owl:Restriction ; - rdfs:subClassOf biolink:SiRNA ; + rdfs:subClassOf biolink:ChemicalToChemicalAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SiRNA . + owl:someValuesFrom biolink:ChemicalToChemicalAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellularComponent ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonSpecialization ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellularComponent . + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonSpecialization . [] a owl:Restriction ; - rdfs:subClassOf biolink:Patent ; + rdfs:subClassOf biolink:Mammal ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Patent . + owl:someValuesFrom biolink:Mammal . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToChemicalAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToChemicalAssociation . + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:label_type ; + owl:onProperty biolink:synonym ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:synonym ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:xref ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneProductMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:WebPage ; + rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:WebPage . + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalProcess ; + rdfs:subClassOf biolink:Cell ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalProcess . + owl:someValuesFrom biolink:Cell . [] a owl:Restriction ; - rdfs:subClassOf biolink:EntityToDiseaseAssociation ; + rdfs:subClassOf biolink:Cohort ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EntityToDiseaseAssociation . + owl:someValuesFrom biolink:Cohort . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToPathwayAssociation ; + rdfs:subClassOf biolink:RetrievalSource ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToPathwayAssociation . + owl:someValuesFrom biolink:RetrievalSource . [] a owl:Restriction ; - rdfs:subClassOf biolink:SocioeconomicExposure ; + rdfs:subClassOf biolink:StudyResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SocioeconomicExposure . + owl:someValuesFrom biolink:StudyResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToChemicalEntityAssociation ; + rdfs:subClassOf biolink:ProteinIsoform ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToChemicalEntityAssociation . + owl:someValuesFrom biolink:ProteinIsoform . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalEntity ; + rdfs:subClassOf biolink:MaterialSampleDerivationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalEntity . + owl:someValuesFrom biolink:MaterialSampleDerivationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalAttribute ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalAttribute . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:Outcome . [] a owl:Restriction ; - rdfs:subClassOf biolink:NucleicAcidEntity ; + rdfs:subClassOf biolink:Phenomenon ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleicAcidEntity . + owl:someValuesFrom biolink:Phenomenon . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToGeneAssociation ; + rdfs:subClassOf biolink:GeographicExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToGeneAssociation . + owl:someValuesFrom biolink:GeographicExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:Mammal ; + rdfs:subClassOf biolink:ClinicalTrial ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Mammal . + owl:someValuesFrom biolink:ClinicalTrial . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugToGeneAssociation ; + rdfs:subClassOf biolink:ReactionToCatalystAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugToGeneAssociation . + owl:someValuesFrom biolink:ReactionToCatalystAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Behavior ; + rdfs:subClassOf biolink:TextMiningResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Behavior . + owl:someValuesFrom biolink:TextMiningResult . [] a owl:Restriction ; rdfs:subClassOf biolink:EnvironmentalProcess ; @@ -13111,139 +13251,156 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:EnvironmentalProcess . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellularOrganism ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellularOrganism . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:NoncodingRNAProduct ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NoncodingRNAProduct . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalSex ; + rdfs:subClassOf biolink:TaxonToTaxonAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalSex . + owl:someValuesFrom biolink:TaxonToTaxonAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Case ; + owl:onProperty biolink:subject ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:CaseToEntityAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToLocationAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:maxCardinality 1 ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ] ; + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityToEntityAssociationMixin . + owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenomicBackgroundExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenomicBackgroundExposure . + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceVariant ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceVariant . + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToChemicalDerivationAssociation ; + rdfs:subClassOf biolink:ObservedExpectedFrequencyAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToChemicalDerivationAssociation . + owl:someValuesFrom biolink:ObservedExpectedFrequencyAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalProcessExposure ; + rdfs:subClassOf biolink:PopulationToPopulationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalProcessExposure . + owl:someValuesFrom biolink:PopulationToPopulationAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:ExposureEvent ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:predicate_type ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ] ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin . + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalEntity ; + rdfs:subClassOf biolink:GrossAnatomicalStructure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalEntity . + owl:someValuesFrom biolink:GrossAnatomicalStructure . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalIntervention ; + rdfs:subClassOf biolink:PhenotypicFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalIntervention . + owl:someValuesFrom biolink:PhenotypicFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalCourse ; + rdfs:subClassOf biolink:MacromolecularMachineToMolecularActivityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalCourse . + owl:someValuesFrom biolink:MacromolecularMachineToMolecularActivityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Agent ; + rdfs:subClassOf biolink:MacromolecularMachineToCellularComponentAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Agent . + owl:someValuesFrom biolink:MacromolecularMachineToCellularComponentAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PopulationToPopulationAssociation ; + rdfs:subClassOf biolink:DatasetSummary ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PopulationToPopulationAssociation . + owl:someValuesFrom biolink:DatasetSummary . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:biological_sequence ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_biological_sequence ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity . + rdfs:subClassOf biolink:GeneToExpressionSiteAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneToExpressionSiteAssociation . [] a owl:Restriction ; rdfs:subClassOf biolink:GeneAsAModelOfDiseaseAssociation ; @@ -13251,54 +13408,73 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:GeneAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularComplex ; + rdfs:subClassOf biolink:Agent ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularComplex . + owl:someValuesFrom biolink:Agent . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularEntity ; + rdfs:subClassOf biolink:PhenotypicQuality ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularEntity . + owl:someValuesFrom biolink:PhenotypicQuality . [] a owl:Restriction ; - rdfs:subClassOf biolink:RegulatoryRegion ; + rdfs:subClassOf biolink:CommonDataElement ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RegulatoryRegion . + owl:someValuesFrom biolink:CommonDataElement . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ActivityAndBehavior . + rdfs:subClassOf biolink:ComplexMolecularMixture ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ComplexMolecularMixture . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PreprintPublication ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PreprintPublication . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GenotypicSex ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GenotypicSex . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:EnvironmentalFoodContaminant ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:EnvironmentalFoodContaminant . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Case ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CaseToEntityAssociationMixin . + owl:someValuesFrom biolink:PathologicalEntityMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Disease ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Disease . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:NucleosomeModification ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:NucleosomeModification . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Plant ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Plant . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ChemicalToPathwayAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ChemicalToPathwayAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:VariantToPopulationAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:VariantToPopulationAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Genome ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Genome . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; @@ -13314,7 +13490,7 @@ biolink:subject a owl:ObjectProperty ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Drug ; + owl:allValuesFrom biolink:CellLine ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; @@ -13322,559 +13498,281 @@ biolink:subject a owl:ObjectProperty ; [ a owl:Restriction ; owl:allValuesFrom biolink:predicate_type ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DrugToEntityAssociationMixin . + owl:someValuesFrom biolink:CellLineToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonInteraction ; + rdfs:subClassOf biolink:MolecularActivityToPathwayAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonInteraction . + owl:someValuesFrom biolink:MolecularActivityToPathwayAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PosttranslationalModification ; + rdfs:subClassOf biolink:Transcript ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PosttranslationalModification . + owl:someValuesFrom biolink:Transcript . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:synonym ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:label_type ; - owl:onProperty biolink:synonym ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:xref ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneProductMixin . + rdfs:subClassOf biolink:ChemicalRole ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ChemicalRole . [] a owl:Restriction ; - rdfs:subClassOf biolink:ReactionToCatalystAssociation ; + rdfs:subClassOf biolink:ConceptCountAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReactionToCatalystAssociation . + owl:someValuesFrom biolink:ConceptCountAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:Phenomenon ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Phenomenon . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:BioticExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BioticExposure . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToDiseaseAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToDiseaseAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceVariantModulatesTreatmentAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceVariantModulatesTreatmentAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Invertebrate ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Invertebrate . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToMolecularActivityAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToMolecularActivityAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Transcript ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Transcript . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:in_taxon_label ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:in_taxon_label ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:label_type ; + owl:onProperty biolink:in_taxon_label ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:in_taxon ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:in_taxon ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:maxCardinality 1 ; + owl:onProperty biolink:in_taxon ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:JournalArticle ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:JournalArticle . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToPhenotypicFeatureAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToPhenotypicFeatureAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalAffectsGeneAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalAffectsGeneAssociation . + owl:someValuesFrom biolink:ThingWithTaxon . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToEnvironmentAssociation ; + rdfs:subClassOf biolink:MacromolecularComplex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToEnvironmentAssociation . + owl:someValuesFrom biolink:MacromolecularComplex . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalProcessOrActivity ; + rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalProcessOrActivity . + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:AdministrativeEntity ; + rdfs:subClassOf biolink:ChemicalMixture ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AdministrativeEntity . + owl:someValuesFrom biolink:ChemicalMixture . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalExposure ; + rdfs:subClassOf biolink:Fungus ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalExposure . + owl:someValuesFrom biolink:Fungus . [] a owl:Restriction ; - rdfs:subClassOf biolink:Drug ; + rdfs:subClassOf biolink:Gene ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Drug . + owl:someValuesFrom biolink:Gene . [] a owl:Restriction ; - rdfs:subClassOf biolink:IndividualOrganism ; + rdfs:subClassOf biolink:NucleicAcidSequenceMotif ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:IndividualOrganism . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:biological_sequence ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_biological_sequence ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EpigenomicEntity . + owl:someValuesFrom biolink:NucleicAcidSequenceMotif . [] a owl:Restriction ; - rdfs:subClassOf biolink:ConceptCountAnalysisResult ; + rdfs:subClassOf biolink:RNAProduct ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ConceptCountAnalysisResult . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:RelationshipQuantifier . + owl:someValuesFrom biolink:RNAProduct . [] a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Occurrent . + owl:someValuesFrom biolink:PhysicalEssenceOrOccurrent . [] a owl:Restriction ; - rdfs:subClassOf biolink:Procedure ; + rdfs:subClassOf biolink:MolecularActivity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Procedure . + owl:someValuesFrom biolink:MolecularActivity . [] a owl:Restriction ; - rdfs:subClassOf biolink:GrossAnatomicalStructure ; + rdfs:subClassOf biolink:ChemicalExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GrossAnatomicalStructure . + owl:someValuesFrom biolink:ChemicalExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneFamily ; + rdfs:subClassOf biolink:OrganismTaxon ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneFamily . + owl:someValuesFrom biolink:OrganismTaxon . [] a owl:Restriction ; - rdfs:subClassOf biolink:NucleicAcidSequenceMotif ; + rdfs:subClassOf biolink:BookChapter ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleicAcidSequenceMotif . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin . + owl:someValuesFrom biolink:BookChapter . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismalEntityAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:Genotype ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismalEntityAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:Genotype . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalProcess ; + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalProcess . + owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation ; + rdfs:subClassOf biolink:Bacterium ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . + owl:someValuesFrom biolink:Bacterium . [] a owl:Restriction ; - rdfs:subClassOf biolink:PopulationOfIndividualOrganisms ; + rdfs:subClassOf biolink:Book ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PopulationOfIndividualOrganisms . + owl:someValuesFrom biolink:Book . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToVariantAssociation ; + rdfs:subClassOf biolink:Onset ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToVariantAssociation . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssenceOrOccurrent . + owl:someValuesFrom biolink:Onset . [] a owl:Restriction ; - rdfs:subClassOf biolink:Haplotype ; + rdfs:subClassOf biolink:DrugExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Haplotype . + owl:someValuesFrom biolink:DrugExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:Cohort ; + rdfs:subClassOf biolink:CellLineAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Cohort . + owl:someValuesFrom biolink:CellLineAsAModelOfDiseaseAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:phenotypic_state ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:phenotypic_state ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:phenotypic_state ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:expression_site ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:expression_site ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:stage_qualifier ], + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:expression_site ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneExpressionMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicSex ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicSex . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:RNAProductIsoform ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RNAProductIsoform . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalMeasurement ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalMeasurement . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:TranscriptToGeneRelationship ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TranscriptToGeneRelationship . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:predicate_type ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:subject ] ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . + owl:someValuesFrom biolink:ChemicalEntityToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntity ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:BehavioralFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntity . + owl:someValuesFrom biolink:BehavioralFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:ComplexMolecularMixture ; + rdfs:subClassOf biolink:SeverityValue ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ComplexMolecularMixture . + owl:someValuesFrom biolink:SeverityValue . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation ; + rdfs:subClassOf biolink:MacromolecularMachineToBiologicalProcessAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . + owl:someValuesFrom biolink:MacromolecularMachineToBiologicalProcessAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ] ; + owl:minCardinality 1 ; + owl:onProperty biolink:id ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FeatureOrDiseaseQualifiersToEntityMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeature . + owl:someValuesFrom biolink:OntologyClass . [] a owl:Restriction ; - rdfs:subClassOf biolink:Treatment ; + rdfs:subClassOf biolink:GeneToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Treatment . + owl:someValuesFrom biolink:GeneToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:TranscriptionFactorBindingSite ; + rdfs:subClassOf biolink:EnvironmentalFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TranscriptionFactorBindingSite . + owl:someValuesFrom biolink:EnvironmentalFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation ; + rdfs:subClassOf biolink:ProteinFamily ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment . + owl:someValuesFrom biolink:ProteinFamily . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToBiologicalProcessAssociation ; + rdfs:subClassOf biolink:VariantAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToBiologicalProcessAssociation . + owl:someValuesFrom biolink:VariantAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalFinding ; + rdfs:subClassOf biolink:PosttranslationalModification ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalFinding . + owl:someValuesFrom biolink:PosttranslationalModification . [] a owl:Restriction ; - rdfs:subClassOf biolink:RetrievalSource ; + rdfs:subClassOf biolink:GenotypeToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RetrievalSource . + owl:someValuesFrom biolink:GenotypeToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Zygosity ; + rdfs:subClassOf biolink:BiologicalSex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Zygosity . + owl:someValuesFrom biolink:BiologicalSex . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:ClinicalCourse ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:ClinicalCourse . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToFeatureOrDiseaseQualifiersMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:NucleosomeModification ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleosomeModification . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToPhenotypicFeatureAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToPhenotypicFeatureAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicLocation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicLocation . + owl:someValuesFrom biolink:ActivityAndBehavior . [] a owl:Restriction ; - rdfs:subClassOf biolink:FunctionalAssociation ; + rdfs:subClassOf biolink:NoncodingRNAProduct ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:FunctionalAssociation . + owl:someValuesFrom biolink:NoncodingRNAProduct . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], @@ -13882,288 +13780,328 @@ biolink:subject a owl:ObjectProperty ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:Drug ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:predicate_type ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:subject ] ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin . + owl:someValuesFrom biolink:DrugToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Exon ; + rdfs:subClassOf biolink:BiologicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Exon . + owl:someValuesFrom biolink:BiologicalEntity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DiseaseToExposureEventAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DiseaseToExposureEventAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:NamedThing ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:NamedThing . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_gene_or_gene_product ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:has_gene_or_gene_product ] ; + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin . + owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Event ; + rdfs:subClassOf biolink:GenotypeAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Event . + owl:someValuesFrom biolink:GenotypeAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ReactionToParticipantAssociation ; + rdfs:subClassOf biolink:StudyPopulation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReactionToParticipantAssociation . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide . + owl:someValuesFrom biolink:StudyPopulation . [] a owl:Restriction ; - rdfs:subClassOf biolink:MicroRNA ; + rdfs:subClassOf biolink:Drug ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MicroRNA . + owl:someValuesFrom biolink:Drug . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:sex_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:BiologicalSex ; owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:predicate_type ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:sex_qualifier ] ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin . -[] a owl:Restriction ; - rdfs:subClassOf biolink:TextMiningResult ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TextMiningResult . - [] a owl:Restriction ; rdfs:subClassOf biolink:DrugLabel ; owl:onProperty biolink:category ; owl:someValuesFrom biolink:DrugLabel . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneFamilyAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneFamilyAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Publication ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Publication . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:DruggableGeneToDiseaseAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DruggableGeneToDiseaseAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:Snv ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:Snv . [] a owl:Restriction ; - rdfs:subClassOf biolink:Cell ; + rdfs:subClassOf biolink:GeneHasVariantThatContributesToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Cell . + owl:someValuesFrom biolink:GeneHasVariantThatContributesToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntity ; + rdfs:subClassOf biolink:PathologicalProcessExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntity . + owl:someValuesFrom biolink:PathologicalProcessExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:Genotype ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Genotype . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:RelationshipQuantifier . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:in_taxon ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:label_type ; - owl:onProperty biolink:in_taxon_label ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:in_taxon_label ], + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:in_taxon ], + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:in_taxon ], + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:in_taxon_label ] ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ThingWithTaxon . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivity . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalAnatomicalExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalAnatomicalExposure . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:BehaviorToBehavioralFeatureAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehaviorToBehavioralFeatureAssociation . + owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Association ; + rdfs:subClassOf biolink:ReagentTargetedGene ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Association . + owl:someValuesFrom biolink:ReagentTargetedGene . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureExposure ; + rdfs:subClassOf biolink:Human ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureExposure . + owl:someValuesFrom biolink:Human . [] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSample ; + rdfs:subClassOf biolink:GeneAffectsChemicalAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSample . + owl:someValuesFrom biolink:GeneAffectsChemicalAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:SocioeconomicAttribute ; + rdfs:subClassOf biolink:ClinicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SocioeconomicAttribute . + owl:someValuesFrom biolink:ClinicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGoTermAssociation ; + rdfs:subClassOf biolink:AdministrativeEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGoTermAssociation . + owl:someValuesFrom biolink:AdministrativeEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneAssociation ; + rdfs:subClassOf biolink:TranscriptToGeneRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneAssociation . + owl:someValuesFrom biolink:TranscriptToGeneRelationship . [] a owl:Restriction ; - rdfs:subClassOf biolink:Article ; + rdfs:subClassOf biolink:GenomicSequenceLocalization ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Article . + owl:someValuesFrom biolink:GenomicSequenceLocalization . [] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetSummary ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetSummary . + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:SequenceVariant ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:VariantToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Bacterium ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Bacterium . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PathognomonicityQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToDiseaseAssociation ; + rdfs:subClassOf biolink:TranscriptionFactorBindingSite ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToDiseaseAssociation . + owl:someValuesFrom biolink:TranscriptionFactorBindingSite . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicQuality ; + rdfs:subClassOf biolink:SocioeconomicAttribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicQuality . + owl:someValuesFrom biolink:SocioeconomicAttribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:BehavioralExposure ; + rdfs:subClassOf biolink:MolecularActivityToChemicalEntityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehavioralExposure . + owl:someValuesFrom biolink:MolecularActivityToChemicalEntityAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Outcome ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:frequency_qualifier ] ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQualifierMixin . + owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinDomain ; + rdfs:subClassOf biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinDomain . + owl:someValuesFrom biolink:PopulationOfIndividualOrganisms . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeographicLocation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeographicLocation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ExonToTranscriptRelationship ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ExonToTranscriptRelationship . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneToGeneProductRelationship ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneToGeneProductRelationship . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:VariantToDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:VariantToDiseaseAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DatasetDistribution ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DatasetDistribution . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:OrganismalEntityAsAModelOfDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismalEntityAsAModelOfDiseaseAssociation . [] a owl:Restriction ; rdfs:subClassOf biolink:Device ; @@ -14171,139 +14109,200 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:Device . [] a owl:Restriction ; - rdfs:subClassOf biolink:EvidenceType ; + rdfs:subClassOf biolink:Invertebrate ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EvidenceType . + owl:someValuesFrom biolink:Invertebrate . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalExposure ; + rdfs:subClassOf biolink:MaterialSample ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalExposure . + owl:someValuesFrom biolink:MaterialSample . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicFeatureToDiseaseAssociation ; + rdfs:subClassOf biolink:Serial ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicFeatureToDiseaseAssociation . + owl:someValuesFrom biolink:Serial . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalAnatomicalStructure ; + rdfs:subClassOf biolink:PathologicalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalAnatomicalStructure . + owl:someValuesFrom biolink:PathologicalProcess . [] a owl:Restriction ; - rdfs:subClassOf biolink:SeverityValue ; + rdfs:subClassOf biolink:MolecularActivityToMolecularActivityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SeverityValue . + owl:someValuesFrom biolink:MolecularActivityToMolecularActivityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ConfidenceLevel ; + rdfs:subClassOf biolink:CausalGeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ConfidenceLevel . + owl:someValuesFrom biolink:CausalGeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiagnosticAid ; + rdfs:subClassOf biolink:ConfidenceLevel ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiagnosticAid . + owl:someValuesFrom biolink:ConfidenceLevel . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxon ; + rdfs:subClassOf biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxon . + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalRole ; + rdfs:subClassOf biolink:GeneToGeneCoexpressionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalRole . + owl:someValuesFrom biolink:GeneToGeneCoexpressionAssociation . [] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:biological_sequence ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_biological_sequence ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneOrGeneProduct . + owl:someValuesFrom biolink:GenomicEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalFeature ; + rdfs:subClassOf biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalFeature . + owl:someValuesFrom biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneToPathwayAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneToPathwayAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ] ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin . + owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:OrganismToOrganismAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismToOrganismAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ] ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin . + owl:someValuesFrom biolink:EntityToFeatureOrDiseaseQualifiersMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Study ; + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Study . + owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicLocationAtTime ; + rdfs:subClassOf biolink:BehaviorToBehavioralFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicLocationAtTime . + owl:someValuesFrom biolink:BehaviorToBehavioralFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:FoodAdditive ; + rdfs:subClassOf biolink:ChemicalEntityAssessesNamedThingAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:FoodAdditive . + owl:someValuesFrom biolink:ChemicalEntityAssessesNamedThingAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PreprintPublication ; + rdfs:subClassOf biolink:Virus ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PreprintPublication . + owl:someValuesFrom biolink:Virus . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Food ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Food . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PlanetaryEntity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PlanetaryEntity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:EntityToDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:EntityToDiseaseAssociation . + +[] a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneProductIsoformMixin . diff --git a/project/shacl/biolink_model.shacl.ttl b/project/shacl/biolink_model.shacl.ttl index 4a08b4742..abd43e01e 100644 --- a/project/shacl/biolink_model.shacl.ttl +++ b/project/shacl/biolink_model.shacl.ttl @@ -10,108 +10,106 @@ biolink:AccessibleDnaRegion a sh:NodeShape ; sh:closed true ; sh:description "A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 6 ; + sh:path biolink:full_name ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 11 ; sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path rdf:type ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 9 ; sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; - sh:path biolink:xref ] ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ] ; sh:targetClass biolink:AccessibleDnaRegion . biolink:Activity a sh:NodeShape ; sh:closed true ; sh:description "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 9 ; sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 8 ; @@ -120,13 +118,15 @@ biolink:Activity a sh:NodeShape ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ] ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:Activity . biolink:ActivityAndBehavior a sh:NodeShape ; @@ -138,37 +138,21 @@ biolink:ActivityAndBehavior a sh:NodeShape ; biolink:AdministrativeEntity a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 9 ; sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 2 ; + sh:path biolink:full_name ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 8 ; @@ -179,207 +163,223 @@ biolink:AdministrativeEntity a sh:NodeShape ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ] ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:AdministrativeEntity . biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "a human-readable description of an entity" ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "a point in time" ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 33 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ] ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ] ; sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityAssociation . biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; @@ -392,139 +392,87 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; sh:order 29 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the structure at a later time" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the structure at an earlier time" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 32 ; sh:path biolink:category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -532,242 +480,294 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ] ; - sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . - -biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "the structure at an earlier time" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 30 ; sh:path biolink:id ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "the structure at a later time" ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . + +biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "the part" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the whole" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:class biolink:AnatomicalEntity ; - sh:description "the part" ; + sh:description "the whole" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 34 ; sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a human-readable description of an entity" ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ] ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ] ; sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . biolink:Annotation a sh:NodeShape ; @@ -780,118 +780,118 @@ biolink:Article a sh:NodeShape ; sh:closed true ; sh:description "a piece of writing on a particular topic presented as a stand-alone section of a larger publication" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 18 ; - sh:path biolink:id ], + sh:order 19 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:rights ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 17 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:volume ], + sh:minCount 1 ; + sh:order 18 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:summary ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 15 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 25 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 15 ; - sh:path biolink:provided_by ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 20 ; + sh:path biolink:category ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:order 21 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:iso_abbreviation ], [ sh:datatype xsd:string ; sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:issue ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 9 ; - sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:volume ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:format ], + [ sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:published_in ], [ sh:class biolink:Agent ; sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:authors ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 8 ; - sh:path biolink:mesh_terms ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 22 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; + sh:order 16 ; + sh:path biolink:full_name ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 9 ; + sh:path biolink:xref ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:summary ], + [ sh:datatype xsd:string ; sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; sh:order 10 ; sh:path dct:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 20 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 5 ; - sh:path biolink:pages ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:iri ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:creation_date ], - [ sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:published_in ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:license ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:full_name ], + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 5 ; + sh:path biolink:pages ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 8 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; sh:description "keywords tagging a publication" ; sh:order 7 ; - sh:path biolink:keywords ], - [ sh:datatype xsd:string ; - sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:iso_abbreviation ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:rights ] ; + sh:path biolink:keywords ] ; sh:targetClass biolink:Article . biolink:Association a sh:NodeShape ; @@ -899,98 +899,55 @@ biolink:Association a sh:NodeShape ; sh:description "A typed association between two entities, supported by evidence" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -998,112 +955,161 @@ biolink:Association a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ] ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:Association . biolink:Bacterium a sh:NodeShape ; sh:closed true ; sh:description "A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and are often motile." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 11 ; + sh:path dct:description ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 8 ; @@ -1114,58 +1120,56 @@ biolink:Bacterium a sh:NodeShape ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; - sh:path biolink:in_taxon_label ] ; + sh:path biolink:in_taxon_label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:Bacterium . biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; @@ -1178,18 +1182,16 @@ biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 46 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 45 ; + sh:path biolink:object_aspect_qualifier ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -1198,283 +1200,281 @@ biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; sh:order 13 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:BehavioralFeature ; - sh:description "behavioral feature that is the object of the association" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_percentage ], + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 44 ; sh:path biolink:subject_direction_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:order 43 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:class biolink:BehavioralFeature ; + sh:description "behavioral feature that is the object of the association" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 47 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:has_total ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:has_count ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 28 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 48 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Behavior ; + sh:description "behavior that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:object_aspect_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 36 ; sh:path dct:description ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Behavior ; - sh:description "behavior that is the subject of the association" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ] ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 25 ; + sh:path biolink:object_namespace ] ; sh:targetClass biolink:BehaviorToBehavioralFeatureAssociation . biolink:BehavioralExposure a sh:NodeShape ; sh:closed true ; sh:description "A behavioral exposure is a factor relating to behavior impacting an individual." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], + sh:property [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; sh:path biolink:has_quantitative_value ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; sh:order 12 ; sh:path rdf:type ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 8 ; sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ] ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:BehavioralExposure . biolink:BehavioralOutcome a sh:NodeShape ; @@ -1486,161 +1486,161 @@ biolink:BehavioralOutcome a sh:NodeShape ; biolink:BiologicalEntity a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 11 ; + sh:path dct:description ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ] ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ] ; sh:targetClass biolink:BiologicalEntity . biolink:BiologicalProcessOrActivity a sh:NodeShape ; sh:closed true ; sh:description "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:order 12 ; sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], [ sh:class biolink:PhysicalEntity ; sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:enabled_by ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 9 ; sh:path biolink:synonym ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_output ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 14 ; + sh:path dct:description ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_input ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_output ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:in_taxon ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:in_taxon_label ] ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path rdfs:label ] ; sh:targetClass biolink:BiologicalProcessOrActivity . biolink:BioticExposure a sh:NodeShape ; sh:closed true ; sh:description "An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -1650,38 +1650,20 @@ biolink:BioticExposure a sh:NodeShape ; sh:maxCount 1 ; sh:order 13 ; sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:category ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -1689,246 +1671,264 @@ biolink:BioticExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 15 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:BioticExposure . - -biolink:Book a sh:NodeShape ; - sh:closed true ; - sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:license ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 21 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ] ; + sh:targetClass biolink:BioticExposure . + +biolink:Book a sh:NodeShape ; + sh:closed true ; + sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 11 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:summary ], [ sh:class biolink:Agent ; sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:authors ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Should generally be set to an ontology class defined term for 'book'." ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ], + sh:description "Books should have industry-standard identifier such as from ISBN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:description "mesh terms tagging a publication" ; sh:order 4 ; sh:path biolink:mesh_terms ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], + sh:order 7 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:format ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "keywords tagging a publication" ; sh:order 3 ; sh:path biolink:keywords ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Should generally be set to an ontology class defined term for 'book'." ; + sh:order 17 ; + sh:path rdf:type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "Books should have industry-standard identifier such as from ISBN." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path biolink:format ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:deprecated ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 1 ; + sh:path biolink:pages ], [ sh:datatype xsd:string ; sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; sh:order 6 ; sh:path dct:type ], - [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:category ] ; + sh:order 15 ; + sh:path biolink:iri ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Book . biolink:BookChapter a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 19 ; - sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:iri ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:property [ sh:description "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:creation_date ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 16 ; - sh:path biolink:synonym ], + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:published_in ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 14 ; - sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:full_name ], + sh:order 24 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:order 9 ; + sh:path dct:type ], [ sh:datatype xsd:string ; sh:order 20 ; sh:path rdf:type ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:authors ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:license ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 22 ; sh:path dct:description ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 21 ; - sh:path rdfs:label ], + sh:order 5 ; + sh:path biolink:summary ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:format ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 7 ; - sh:path biolink:mesh_terms ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:has_attribute ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 7 ; + sh:path biolink:mesh_terms ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 16 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 9 ; - sh:path dct:type ], + sh:order 17 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 4 ; + sh:path biolink:pages ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:full_name ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:volume ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:license ], - [ sh:description "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN." ; - sh:maxCount 1 ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:published_in ], + sh:order 19 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:description "chapter of a book" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:summary ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:authors ], + sh:order 2 ; + sh:path biolink:chapter ], [ sh:datatype xsd:string ; sh:description "keywords tagging a publication" ; sh:order 6 ; sh:path biolink:keywords ], - [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "chapter of a book" ; + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:chapter ], + sh:order 21 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 4 ; - sh:path biolink:pages ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:deprecated ] ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 14 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:BookChapter . biolink:CaseToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "An abstract association for use where the case is the subject" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:class biolink:Case ; sh:description "the case (e.g. patient) that has the property" ; sh:maxCount 1 ; @@ -1942,163 +1942,154 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; + sh:property [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 48 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:has_count ], - [ sh:class biolink:Case ; - sh:description "the case (e.g. patient) that has the property" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_quotient ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_direction_qualifier ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 45 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 34 ; sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:order 40 ; sh:path biolink:has_total ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 38 ; sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Case ; + sh:description "the case (e.g. patient) that has the property" ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 17 ; sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 44 ; sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 36 ; sh:path dct:description ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 31 ; + sh:path biolink:id ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -2106,165 +2097,179 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:has_count ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 46 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 33 ; sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 47 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 35 ; sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 32 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ] ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ] ; sh:targetClass biolink:CaseToPhenotypicFeatureAssociation . biolink:CausalGeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], + sh:order 44 ; + sh:path biolink:has_percentage ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:datatype xsd:double ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 40 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_total ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], + sh:order 20 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is shown to cause the disease." ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 19 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:order 47 ; sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 48 ; @@ -2276,185 +2281,177 @@ biolink:CausalGeneToDiseaseAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is shown to cause the disease." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ], + sh:order 43 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:p_value ], + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 35 ; + sh:path biolink:category ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 45 ; sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:boolean ; + sh:order 34 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 39 ; + sh:path biolink:has_attribute ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], + sh:order 42 ; + sh:path biolink:has_total ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 33 ; - sh:path biolink:id ], + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:primary_knowledge_source ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path dct:description ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:order 41 ; sh:path biolink:has_count ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_percentage ], - [ sh:description "a point in time" ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:order 33 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path dct:description ] ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:object_label_closure ] ; sh:targetClass biolink:CausalGeneToDiseaseAssociation . biolink:Cell a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; @@ -2463,182 +2460,214 @@ biolink:Cell a sh:NodeShape ; [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; - sh:path dct:description ] ; + sh:path dct:description ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:Cell . biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:order 40 ; sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:CellLine ; - sh:description "A cell line derived from an organismal entity with a disease state that is used as a model of that disease." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 38 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "The relationship to the disease" ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:CellLine ; + sh:description "A cell line derived from an organismal entity with a disease state that is used as a model of that disease." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 43 ; sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 42 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 34 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 39 ; sh:path biolink:subject_direction_qualifier ], - [ sh:description "a human-readable description of an entity" ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -2646,270 +2675,241 @@ biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:order 18 ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:subject_aspect_qualifier ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:qualified_predicate ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "The relationship to the disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 31 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:CellLineAsAModelOfDiseaseAssociation . + +biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ] ; - sh:targetClass biolink:CellLineAsAModelOfDiseaseAssociation . - -biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 30 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 32 ; sh:path biolink:category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 31 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ] ; + sh:order 28 ; + sh:path biolink:p_value ] ; sh:targetClass biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . biolink:CellLineToEntityAssociationMixin a sh:NodeShape ; @@ -2941,141 +2941,122 @@ biolink:CellularOrganism a sh:NodeShape ; sh:closed true ; sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 5 ; sh:path biolink:synonym ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ] ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ] ; sh:targetClass biolink:CellularOrganism . biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 49 ; - sh:path rdfs:label ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:causal_mechanism_qualifier ], + sh:order 50 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 45 ; - sh:path biolink:id ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 25 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 17 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 52 ; + sh:path biolink:deprecated ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:object_category ], + sh:order 28 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:subject_namespace ], + sh:order 24 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 14 ; + sh:path biolink:species_context_qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:publications ], + sh:order 51 ; + sh:path biolink:has_attribute ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 47 ; sh:path biolink:category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:subject_category ], [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; @@ -3087,345 +3068,359 @@ biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:anatomical_context_qualifier ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:knowledge_source ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:species_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 41 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 42 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:p_value ], + sh:order 49 ; + sh:path rdfs:label ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 30 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 52 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 50 ; - sh:path dct:description ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path rdf:predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:has_evidence ], + sh:order 46 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:subject_category ], + sh:order 33 ; + sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:subject_category_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 35 ; sh:path biolink:object_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 27 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 25 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:knowledge_source ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:object_part_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 34 ; - sh:path biolink:subject_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:object_namespace ], + sh:order 9 ; + sh:path biolink:object_context_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 40 ; sh:path biolink:subject_label_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path rdf:subject ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:object_context_qualifier ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 48 ; sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:negated ], + sh:order 38 ; + sh:path biolink:subject_namespace ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 41 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:subject_context_qualifier ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path rdf:predicate ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:qualified_predicate ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:object_part_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 44 ; + sh:path biolink:adjusted_p_value ], [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:subject_part_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:original_object ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 26 ; - sh:path biolink:knowledge_level ], - [ sh:description "a point in time" ; + sh:order 27 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:timepoint ], + sh:order 43 ; + sh:path biolink:p_value ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:object_aspect_qualifier ], [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; sh:in ( "metabolite" ) ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:subject_derivative_qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 51 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:ChemicalAffectsGeneAssociation . - -biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:order 6 ; + sh:path biolink:object_form_or_variant_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 24 ; + sh:order 39 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 31 ; + sh:path biolink:original_object ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 17 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; + sh:order 45 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 34 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 5 ; + sh:order 20 ; sh:path biolink:qualifiers ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:order 21 ; sh:path biolink:publications ], + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; + sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:causal_mechanism_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:object_category_closure ] ; + sh:targetClass biolink:ChemicalAffectsGeneAssociation . + +biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 31 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 33 ; sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 13 ; @@ -3435,233 +3430,238 @@ biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ] ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ] ; sh:targetClass biolink:ChemicalEntityAssessesNamedThingAssociation . biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "A regulatory relationship between two genes" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "the direction is always from regulator to regulated" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 25 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 17 ; sh:path biolink:original_object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 6 ; + sh:path biolink:qualifiers ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:negated ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "the direction is always from regulator to regulated" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:subject_category_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 1 ; - sh:path rdf:subject ], + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ] ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ] ; sh:targetClass biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . biolink:ChemicalEntityOrProteinOrPolypeptide a sh:NodeShape ; @@ -3681,146 +3681,191 @@ biolink:ChemicalEntityToEntityAssociationMixin a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ] ; + sh:path rdf:object ] ; sh:targetClass biolink:ChemicalEntityToEntityAssociationMixin . biolink:ChemicalExposure a sh:NodeShape ; sh:closed true ; sh:description "A chemical exposure is an intake of a particular chemical entity." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path biolink:timepoint ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path biolink:has_quantitative_value ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:full_name ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:timepoint ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path biolink:has_quantitative_value ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 2 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:has_attribute_type ] ; + sh:path biolink:has_attribute_type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ] ; sh:targetClass biolink:ChemicalExposure . biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; sh:closed true ; sh:description "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:original_subject ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 10 ; + sh:path rdf:object ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 40 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 41 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:knowledge_source ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 42 ; sh:path rdfs:label ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_form_or_variant_qualifier ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 44 ; sh:path biolink:has_attribute ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:original_subject ], + sh:order 37 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category ], + sh:order 25 ; + sh:path biolink:subject_category ], [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:object_context_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:qualifiers ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -3828,32 +3873,77 @@ biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 20 ; sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 33 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:object_namespace ], [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:object_part_qualifier ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_evidence ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], - [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; - sh:in ( "metabolite" ) ; + sh:order 39 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_derivative_qualifier ], + sh:order 31 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:primary_knowledge_source ], + sh:order 12 ; + sh:path biolink:qualifier ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category ], + sh:order 3 ; + sh:path biolink:subject_context_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:negated ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_part_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 34 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 38 ; + sh:path biolink:id ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -3861,248 +3951,158 @@ biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 19 ; sh:path biolink:knowledge_level ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; + sh:in ( "metabolite" ) ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 2 ; + sh:path biolink:subject_derivative_qualifier ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 10 ; - sh:path rdf:object ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:order 43 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 17 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:order 9 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 41 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 33 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 38 ; - sh:path biolink:id ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:subject_context_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 34 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:negated ], + sh:order 13 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 45 ; sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:object_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 14 ; + sh:path biolink:publications ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:iri ], + sh:order 36 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 18 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 9 ; - sh:path rdf:predicate ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:subject_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:timepoint ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:original_predicate ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 40 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:AnatomicalEntity ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:adjusted_p_value ] ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:anatomical_context_qualifier ] ; sh:targetClass biolink:ChemicalGeneInteractionAssociation . biolink:ChemicalMixture a sh:NodeShape ; sh:closed true ; sh:description "A chemical mixture is a chemical entity composed of two or more molecular entities." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 12 ; + sh:path biolink:synonym ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 17 ; sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 12 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:is_supplement ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:category ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], [ sh:datatype xsd:string ; - sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:iri ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], + sh:order 4 ; + sh:path biolink:trade_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:is_toxic ], - [ sh:datatype xsd:string ; - sh:order 16 ; - sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:category ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ], + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:trade_name ] ; + sh:path biolink:has_chemical_role ] ; sh:targetClass biolink:ChemicalMixture . biolink:ChemicalOrDrugOrTreatment a sh:NodeShape ; @@ -4114,36 +4114,17 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation sh:closed true ; sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "disease or phenotype" ; sh:maxCount 1 ; @@ -4151,102 +4132,89 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:qualifiers ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 35 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 25 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 31 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:description "" ; - sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:FDA_adverse_event_level ], + sh:order 29 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], + sh:order 22 ; + sh:path biolink:subject_category_closure ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -4254,15 +4222,15 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation sh:minCount 1 ; sh:order 13 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; @@ -4274,76 +4242,122 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:description "" ; + sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:FDA_adverse_event_level ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 28 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 7 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ] ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:description "" ; - sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:FDA_adverse_event_level ], - [ sh:description "a point in time" ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "disease or phenotype" ; sh:maxCount 1 ; @@ -4352,8 +4366,24 @@ biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:No sh:order 3 ; sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; sh:path biolink:subject_label_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; @@ -4365,175 +4395,155 @@ biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:No sh:maxCount 1 ; sh:order 29 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], + sh:order 13 ; + sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:qualifiers ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "" ; + sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 0 ; + sh:path biolink:FDA_adverse_event_level ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], + sh:order 14 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 25 ; sh:path biolink:object_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 17 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path dct:description ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ] ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 33 ; + sh:path biolink:category ] ; sh:targetClass biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . biolink:ChemicalToChemicalAssociation a sh:NodeShape ; sh:closed true ; sh:description "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -4542,363 +4552,353 @@ biolink:ChemicalToChemicalAssociation a sh:NodeShape ; sh:order 12 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical element that is the target of the statement" ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ] ; + sh:order 11 ; + sh:path biolink:knowledge_level ] ; sh:targetClass biolink:ChemicalToChemicalAssociation . biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; sh:closed true ; sh:description "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 catalyst qualifier P" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the downstream chemical entity" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:publications ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical." ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path biolink:catalyst_qualifier ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the upstream chemical entity" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], + sh:order 22 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:description "a point in time" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 33 ; sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical." ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path biolink:catalyst_qualifier ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], + sh:order 29 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], + sh:order 17 ; + sh:path biolink:original_object ], [ sh:class biolink:ChemicalEntity ; - sh:description "the downstream chemical entity" ; + sh:description "the upstream chemical entity" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:original_subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 32 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ] ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:subject_namespace ] ; sh:targetClass biolink:ChemicalToChemicalDerivationAssociation . biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; @@ -4906,193 +4906,193 @@ biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:description "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 3 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; sh:path biolink:negated ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "the disease or phenotype that is affected by the chemical" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_attribute ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a point in time" ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "the disease or phenotype that is affected by the chemical" ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 33 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ] ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . biolink:ChemicalToEntityAssociationMixin a sh:NodeShape ; @@ -5106,167 +5106,84 @@ biolink:ChemicalToEntityAssociationMixin a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ] ; + sh:path rdf:object ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:ChemicalToEntityAssociationMixin . biolink:ChemicalToPathwayAssociation a sh:NodeShape ; sh:closed true ; sh:description "An interaction between a chemical entity and a biological process or pathway." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical entity that is affecting the pathway" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "a point in time" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical entity that is affecting the pathway" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:Pathway ; sh:description "the pathway that is affected by the chemical" ; sh:maxCount 1 ; @@ -5274,84 +5191,169 @@ biolink:ChemicalToPathwayAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ] ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ] ; sh:targetClass biolink:ChemicalToPathwayAssociation . biolink:ChiSquaredAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a chi squared analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 8 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; @@ -5362,28 +5364,26 @@ biolink:ChiSquaredAnalysisResult a sh:NodeShape ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], + sh:order 12 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ] ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ] ; sh:targetClass biolink:ChiSquaredAnalysisResult . biolink:ClinicalCourse a sh:NodeShape ; @@ -5391,21 +5391,42 @@ biolink:ClinicalCourse a sh:NodeShape ; sh:description "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; sh:order 11 ; sh:path rdf:type ], @@ -5416,19 +5437,9 @@ biolink:ClinicalCourse a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 12 ; @@ -5437,26 +5448,15 @@ biolink:ClinicalCourse a sh:NodeShape ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 0 ; sh:path rdfs:label ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ] ; + sh:order 13 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:ClinicalCourse . biolink:ClinicalEntity a sh:NodeShape ; @@ -5464,153 +5464,130 @@ biolink:ClinicalEntity a sh:NodeShape ; sh:description "Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path dct:description ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 8 ; sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ] ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:ClinicalEntity . biolink:ClinicalFinding a sh:NodeShape ; sh:closed true ; sh:description "this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:ClinicalAttribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:ClinicalFinding . - -biolink:ClinicalIntervention a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; - sh:path biolink:synonym ], + sh:path biolink:xref ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; + sh:order 11 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:class biolink:ClinicalAttribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:ClinicalFinding . + +biolink:ClinicalIntervention a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 6 ; @@ -5618,55 +5595,97 @@ biolink:ClinicalIntervention a sh:NodeShape ; [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ] ; + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:ClinicalIntervention . biolink:ClinicalMeasurement a sh:NodeShape ; sh:closed true ; sh:description "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 0 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -5674,60 +5693,35 @@ biolink:ClinicalMeasurement a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:class biolink:QuantityValue ; + [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ] ; + sh:order 12 ; + sh:path dct:description ] ; sh:targetClass biolink:ClinicalMeasurement . biolink:ClinicalModifier a sh:NodeShape ; sh:closed true ; sh:description "Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:QuantityValue ; + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -5735,197 +5729,204 @@ biolink:ClinicalModifier a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:deprecated ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 12 ; sh:path dct:description ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 0 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ] ; + sh:path rdfs:label ] ; sh:targetClass biolink:ClinicalModifier . biolink:ClinicalTrial a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:deprecated ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; - sh:path biolink:provided_by ] ; + sh:path biolink:provided_by ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path dct:description ] ; sh:targetClass biolink:ClinicalTrial . biolink:CodingSequence a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 4 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:has_biological_sequence ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 9 ; sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:order 10 ; sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 6 ; - sh:path biolink:synonym ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 7 ; sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ] ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:CodingSequence . biolink:Cohort a sh:NodeShape ; sh:closed true ; sh:description "A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; @@ -5937,44 +5938,44 @@ biolink:Cohort a sh:NodeShape ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ] ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ] ; sh:targetClass biolink:Cohort . biolink:CommonDataElement a sh:NodeShape ; sh:closed true ; sh:description "A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. (https://cde.nlm.nih.gov/home)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:order 11 ; sh:path rdf:type ], @@ -5982,45 +5983,48 @@ biolink:CommonDataElement a sh:NodeShape ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 10 ; sh:path biolink:category ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path biolink:rights ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 0 ; @@ -6028,23 +6032,26 @@ biolink:CommonDataElement a sh:NodeShape ; [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 12 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ] ; + sh:path rdfs:label ] ; sh:targetClass biolink:CommonDataElement . biolink:ComplexChemicalExposure a sh:NodeShape ; sh:closed true ; sh:description "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 12 ; @@ -6052,46 +6059,24 @@ biolink:ComplexChemicalExposure a sh:NodeShape ; [ sh:datatype xsd:string ; sh:order 11 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 0 ; sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:QuantityValue ; + [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; @@ -6100,339 +6085,377 @@ biolink:ComplexChemicalExposure a sh:NodeShape ; sh:minCount 1 ; sh:order 10 ; sh:path biolink:category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ] ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ] ; sh:targetClass biolink:ComplexChemicalExposure . biolink:ComplexMolecularMixture a sh:NodeShape ; sh:closed true ; sh:description "A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; - sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], + sh:order 18 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:id ], + sh:order 4 ; + sh:path biolink:trade_name ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "" ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], + sh:order 7 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:trade_name ], + sh:order 0 ; + sh:path biolink:is_supplement ], [ sh:datatype xsd:string ; - sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 12 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:id ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:order 16 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:description "a human-readable description of an entity" ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 17 ; + sh:path rdfs:label ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:datatype xsd:string ; + sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:iri ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 10 ; sh:path biolink:xref ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 12 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:order 20 ; + sh:path biolink:deprecated ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ] ; + sh:order 14 ; + sh:path biolink:iri ] ; sh:targetClass biolink:ComplexMolecularMixture . biolink:ConceptCountAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a concept count analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 7 ; sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:creation_date ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:format ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], + sh:order 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ] ; + sh:order 9 ; + sh:path biolink:iri ] ; sh:targetClass biolink:ConceptCountAnalysisResult . biolink:ConfidenceLevel a sh:NodeShape ; sh:closed true ; sh:description "Level of confidence in a statement" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:format ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:rights ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 12 ; sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ] ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ] ; sh:targetClass biolink:ConfidenceLevel . biolink:ContributorAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a point in time" ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:object_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 35 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:InformationContentEntity ; + sh:description "information content entity which an agent has helped realise" ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; - sh:description "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -6440,339 +6463,311 @@ biolink:ContributorAssociation a sh:NodeShape ; sh:order 17 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:description "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:InformationContentEntity ; - sh:description "information content entity which an agent has helped realise" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 34 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 30 ; sh:path biolink:id ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:Agent ; sh:description "agent helping to realise the given entity (e.g. such as a publication)" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ] ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:ContributorAssociation . biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:subject_category ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 33 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_total ], + sh:order 40 ; + sh:path biolink:deprecated ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is shown to correlate with the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 36 ; - sh:path rdf:type ], + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 35 ; + sh:path biolink:category ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:p_value ], + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 45 ; sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_count ], - [ sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path dct:description ], + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:description "a point in time" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], + sh:order 47 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:double ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_quotient ], + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 37 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 18 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 34 ; sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 36 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:publications ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is shown to correlate with the disease." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category_closure ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 48 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 31 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 35 ; - sh:path biolink:category ], + sh:order 17 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], + sh:order 33 ; + sh:path biolink:id ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -6780,268 +6775,264 @@ biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 15 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:deprecated ] ; + sh:order 44 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:has_quotient ] ; sh:targetClass biolink:CorrelatedGeneToDiseaseAssociation . biolink:DatasetSummary a sh:NodeShape ; sh:closed true ; sh:description "an item that holds summary level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:format ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:order 13 ; - sh:path rdf:type ], + sh:order 17 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:source_web_page ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 2 ; + sh:path biolink:license ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 5 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 14 ; - sh:path rdfs:label ], + sh:order 4 ; + sh:path biolink:format ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:license ], + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path dct:description ], + sh:order 3 ; + sh:path biolink:rights ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:rights ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 1 ; sh:path schema1:logo ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 9 ; - sh:path biolink:synonym ] ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:order 13 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:category ] ; sh:targetClass biolink:DatasetSummary . biolink:DatasetVersion a sh:NodeShape ; sh:closed true ; sh:description "an item that holds version level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:class biolink:DatasetDistribution ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path dct:distribution ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 16 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:id ], [ sh:class biolink:Dataset ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_dataset ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:ingest_date ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 18 ; sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:class biolink:DatasetDistribution ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path dct:distribution ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:format ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:iri ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 10 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:order 14 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:rights ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:order 14 ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:license ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ] ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:ingest_date ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:DatasetVersion . biolink:DiagnosticAid a sh:NodeShape ; sh:closed true ; sh:description "A device or substance used to help diagnose disease or injury" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ] ; + sh:order 7 ; + sh:path rdf:type ] ; sh:targetClass biolink:DiagnosticAid . biolink:DiseaseOrPhenotypicFeatureExposure a sh:NodeShape ; sh:closed true ; sh:description "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 7 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:description "a point in time" ; + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 1 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -7049,44 +7040,53 @@ biolink:DiseaseOrPhenotypicFeatureExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ] ; + sh:order 13 ; + sh:path dct:description ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeatureExposure . biolink:DiseaseOrPhenotypicFeatureOutcome a sh:NodeShape ; @@ -7098,7 +7098,14 @@ biolink:DiseaseOrPhenotypicFeatureOutcome a sh:NodeShape ; biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:property [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; @@ -7109,14 +7116,7 @@ biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; + sh:path rdf:object ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape ; @@ -7124,9 +7124,11 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape sh:description "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "disease or phenotype" ; sh:maxCount 1 ; @@ -7134,61 +7136,30 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:GeneticInheritance ; sh:description "genetic inheritance associated with the specified disease or phenotypic feature." ; sh:maxCount 1 ; @@ -7196,32 +7167,72 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; @@ -7234,318 +7245,374 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape sh:order 17 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 31 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . + +biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ] ; - sh:targetClass biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . - -biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "anatomical entity in which the disease or feature is found." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 35 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 23 ; sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "a point in time" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "anatomical entity in which the disease or feature is found." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; + sh:targetClass biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . + +biolink:DiseaseToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Disease ; + sh:description "disease class" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ] ; + sh:targetClass biolink:DiseaseToEntityAssociationMixin . + +biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between an exposure event and a disease." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; - sh:targetClass biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . - -biolink:DiseaseToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Disease ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Disease ; sh:description "disease class" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:DiseaseToEntityAssociationMixin . - -biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between an exposure event and a disease." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -7553,238 +7620,230 @@ biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:ExposureEvent ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Disease ; - sh:description "disease class" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:description "a point in time" ; sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:ExposureEvent ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 2 ; + sh:path rdf:object ] ; + sh:targetClass biolink:DiseaseToExposureEventAssociation . + +biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 47 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:order 15 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:has_total ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 15 ; + sh:order 21 ; sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 34 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 43 ; + sh:path biolink:deprecated ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path biolink:timepoint ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 38 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; + sh:order 29 ; sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ] ; - sh:targetClass biolink:DiseaseToExposureEventAssociation . - -biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 16 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "a human-readable description of an entity" ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path dct:description ], + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:subject_category ], [ sh:class biolink:Onset ; sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:onset_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:has_attribute ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 1 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], + sh:order 20 ; + sh:path biolink:original_subject ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path rdf:predicate ], - [ sh:datatype xsd:double ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 31 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:has_quotient ], + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; @@ -7793,206 +7852,176 @@ biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 32 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 18 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 40 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 31 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:negated ], + sh:order 42 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 36 ; sh:path biolink:id ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:timepoint ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_direction_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 28 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 9 ; + sh:path biolink:negated ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:subject_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 39 ; - sh:path rdf:type ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:sex_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:Disease ; + sh:description "disease class" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category ], + sh:order 5 ; + sh:path rdf:subject ], [ sh:datatype xsd:double ; sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:has_percentage ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Disease ; - sh:description "disease class" ; + sh:order 3 ; + sh:path biolink:has_quotient ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:subject ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 18 ; + sh:path biolink:agent_type ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_total ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 41 ; + sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:original_subject ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 38 ; - sh:path biolink:category ], + sh:order 37 ; + sh:path biolink:iri ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category ], + sh:order 11 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 22 ; sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path rdf:object ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:p_value ], + sh:order 17 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 10 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:has_count ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 39 ; + sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:iri ] ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 16 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:publications ] ; sh:targetClass biolink:DiseaseToPhenotypicFeatureAssociation . biolink:DrugExposure a sh:NodeShape ; sh:closed true ; sh:description "A drug exposure is an intake of a particular drug." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; + sh:property [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_attribute_type ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path rdfs:label ], + [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:timepoint ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 11 ; @@ -8002,95 +8031,100 @@ biolink:DrugExposure a sh:NodeShape ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:iri ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 7 ; sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 1 ; - sh:path biolink:has_quantitative_value ] ; + sh:path dct:description ] ; sh:targetClass biolink:DrugExposure . biolink:DrugLabel a sh:NodeShape ; sh:closed true ; sh:description "a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific instructions or warnings for administration, storage and disposal instructions, etc." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:rights ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; sh:order 6 ; sh:path dct:type ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], + sh:order 19 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:summary ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:format ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:order 10 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:format ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:order 17 ; sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 4 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; sh:description "keywords tagging a publication" ; sh:order 3 ; @@ -8099,6 +8133,10 @@ biolink:DrugLabel a sh:NodeShape ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 11 ; sh:path biolink:provided_by ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; @@ -8110,60 +8148,17 @@ biolink:DrugLabel a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:authors ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:rights ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 7 ; - sh:path biolink:license ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:deprecated ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ] ; + sh:path biolink:license ] ; sh:targetClass biolink:DrugLabel . biolink:DrugToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "An interaction between a drug and another entity" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; @@ -8176,81 +8171,132 @@ biolink:DrugToEntityAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path rdf:subject ] ; + sh:path rdf:subject ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:DrugToEntityAssociationMixin . biolink:DrugToGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "An interaction between a drug and a gene or gene product." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:property [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 32 ; sh:path biolink:category ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_attribute ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "a human-readable description of an entity" ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 31 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:Drug ; sh:description "the drug that is an interactor" ; sh:maxCount 1 ; @@ -8259,105 +8305,61 @@ biolink:DrugToGeneAssociation a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 34 ; sh:path rdfs:label ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the gene or gene product that is affected by the drug" ; sh:maxCount 1 ; @@ -8366,365 +8368,369 @@ biolink:DrugToGeneAssociation a sh:NodeShape ; sh:order 2 ; sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ] ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ] ; sh:targetClass biolink:DrugToGeneAssociation . biolink:DrugToGeneInteractionExposure a sh:NodeShape ; sh:closed true ; sh:description "drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 8 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 9 ; - sh:path biolink:xref ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 7 ; sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 11 ; - sh:path biolink:synonym ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:full_name ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_attribute_type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:deprecated ], - [ sh:class biolink:NamedThing ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:category ], + [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:order 13 ; - sh:path rdf:type ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 11 ; + sh:path biolink:synonym ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:order 1 ; + sh:path biolink:timepoint ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_attribute_type ], + sh:order 5 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:order 13 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 8 ; + sh:path biolink:provided_by ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 3 ; sh:path rdfs:label ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:timepoint ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 9 ; + sh:path biolink:xref ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ] ; + sh:order 10 ; + sh:path biolink:full_name ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ] ; sh:targetClass biolink:DrugToGeneInteractionExposure . biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 33 ; sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 20 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], + sh:order 27 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:double ; sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:order 44 ; sh:path biolink:has_percentage ], + [ sh:description "connects an association to an instance of supporting evidence" ; + sh:in ( "tclin" "tbio" "tchem" "tdark" ) ; + sh:order 10 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 32 ; sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state." ; + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:has_quotient ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 18 ; sh:path biolink:original_predicate ], - [ sh:description "connects an association to an instance of supporting evidence" ; - sh:in ( "tclin" "tbio" "tchem" "tdark" ) ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:p_value ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 48 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:order 41 ; sh:path biolink:has_count ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 17 ; + sh:path biolink:original_subject ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:timepoint ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:datatype xsd:double ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_quotient ], + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:order 47 ; sh:path biolink:qualified_predicate ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:iri ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:publications ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ], + sh:order 31 ; + sh:path biolink:p_value ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 35 ; sh:path biolink:category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], + sh:order 7 ; + sh:path biolink:qualifier ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 38 ; sh:path dct:description ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 26 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:retrieval_source_ids ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:deprecated ] ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:DruggableGeneToDiseaseAssociation . biolink:Entity a sh:NodeShape ; sh:closed false ; sh:description "Root Biolink Model class for all things and informational relationships, real or imagined." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_attribute ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 2 ; sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:order 3 ; - sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:order 3 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:id ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path dct:description ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 4 ; @@ -8732,68 +8738,101 @@ biolink:Entity a sh:NodeShape ; [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 1 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ] ; + sh:path biolink:iri ] ; sh:targetClass biolink:Entity . biolink:EntityToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 26 ; sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 32 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 30 ; sh:path biolink:p_value ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:max_research_phase ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path rdf:predicate ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:order 37 ; + sh:path dct:description ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:object ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -8801,100 +8840,73 @@ biolink:EntityToDiseaseAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:agent_type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:subject_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 25 ; sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:qualifiers ], [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + sh:order 2 ; + sh:path rdf:subject ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_subject ], - [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:max_research_phase ], + sh:order 5 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path rdf:predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:negated ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 17 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:object_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:subject ], [ sh:description "" ; sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; sh:maxCount 1 ; @@ -8905,108 +8917,94 @@ biolink:EntityToDiseaseAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 39 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:knowledge_level ] ; + sh:targetClass biolink:EntityToDiseaseAssociation . + +biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:description "mixin class for any association whose object (target node) is a disease" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 2 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:knowledge_source ] ; - sh:targetClass biolink:EntityToDiseaseAssociation . - -biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:description "mixin class for any association whose object (target node) is a disease" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:minCount 1 ; + sh:order 7 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path rdf:object ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:object_direction_qualifier ], + sh:order 6 ; + sh:path rdf:subject ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:qualified_predicate ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:object_aspect_qualifier ] ; + sh:order 3 ; + sh:path biolink:object_direction_qualifier ] ; sh:targetClass biolink:EntityToDiseaseAssociationMixin . biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "disease or phenotype" ; sh:maxCount 1 ; @@ -9014,25 +9012,20 @@ biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ] ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . biolink:EntityToExposureEventAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "An association between some entity and an exposure event." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:ExposureEvent ; + sh:property [ sh:class biolink:ExposureEvent ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; @@ -9043,32 +9036,21 @@ biolink:EntityToExposureEventAssociationMixin a sh:NodeShape ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; - sh:path rdf:predicate ] ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:EntityToExposureEventAssociationMixin . biolink:EntityToFeatureOrDiseaseQualifiersMixin a sh:NodeShape ; sh:closed false ; sh:description "Qualifiers for entity to disease or phenotype associations." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path rdf:object ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:order 4 ; @@ -9079,87 +9061,155 @@ biolink:EntityToFeatureOrDiseaseQualifiersMixin a sh:NodeShape ; sh:order 7 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 2 ; + sh:path biolink:object_aspect_qualifier ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path rdf:subject ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:subject_direction_qualifier ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:object_aspect_qualifier ] ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path rdf:object ] ; sh:targetClass biolink:EntityToFeatureOrDiseaseQualifiersMixin . biolink:EntityToOutcomeAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "An association between some entity and an outcome" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:property [ sh:class biolink:Outcome ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:Outcome ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ] ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:EntityToOutcomeAssociationMixin . biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "" ; - sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; + sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:clinical_approval_status ], + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 35 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:subject_category ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 26 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 25 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 3 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 5 ; + sh:path biolink:negated ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; @@ -9171,183 +9221,120 @@ biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 39 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:object_label_closure ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:object_closure ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:subject ], + [ sh:description "" ; + sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:clinical_approval_status ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:negated ], - [ sh:description "a human-readable description of an entity" ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], + sh:order 33 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:order 16 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:qualifiers ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:max_research_phase ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:object_category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:qualifier ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 38 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 1 ; + sh:path biolink:max_research_phase ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 23 ; + sh:path biolink:subject_category_closure ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:subject ], + sh:order 13 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ] ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ] ; sh:targetClass biolink:EntityToPhenotypicFeatureAssociation . biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:qualified_predicate ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:subject_aspect_qualifier ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -9355,32 +9342,36 @@ biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:has_percentage ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:sex_qualifier ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:has_count ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 5 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 7 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:qualified_predicate ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; @@ -9398,57 +9389,55 @@ biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:has_total ] ; + sh:order 10 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:has_quotient ] ; sh:targetClass biolink:EntityToPhenotypicFeatureAssociationMixin . biolink:EnvironmentalExposure a sh:NodeShape ; sh:closed true ; sh:description "A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], + sh:property [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:timepoint ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 10 ; sh:path biolink:synonym ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -9461,42 +9450,62 @@ biolink:EnvironmentalExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 7 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ] ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ] ; sh:targetClass biolink:EnvironmentalExposure . biolink:EnvironmentalFeature a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 2 ; @@ -9505,31 +9514,22 @@ biolink:EnvironmentalFeature a sh:NodeShape ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 3 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], + sh:order 9 ; + sh:path dct:description ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 8 ; @@ -9539,25 +9539,38 @@ biolink:EnvironmentalFeature a sh:NodeShape ; biolink:EnvironmentalFoodContaminant a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:id ], + sh:order 7 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ], + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:trade_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:id ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path dct:description ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 11 ; @@ -9566,106 +9579,93 @@ biolink:EnvironmentalFoodContaminant a sh:NodeShape ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 1 ; sh:path biolink:available_from ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:is_toxic ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:max_tolerated_dose ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 10 ; - sh:path biolink:iri ] ; + sh:path biolink:iri ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path rdfs:label ] ; sh:targetClass biolink:EnvironmentalFoodContaminant . biolink:EnvironmentalProcess a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], + sh:order 8 ; + sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:order 9 ; sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ] ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ] ; sh:targetClass biolink:EnvironmentalProcess . biolink:EpidemiologicalOutcome a sh:NodeShape ; @@ -9687,41 +9687,46 @@ biolink:Event a sh:NodeShape ; sh:closed true ; sh:description "Something that happens at a given place and time." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 9 ; sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 2 ; @@ -9730,78 +9735,72 @@ biolink:Event a sh:NodeShape ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:Event . biolink:ExonToTranscriptRelationship a sh:NodeShape ; sh:closed true ; sh:description "A transcript is formed from multiple exons" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Exon ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 30 ; sh:path biolink:id ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Transcript ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -9809,106 +9808,111 @@ biolink:ExonToTranscriptRelationship a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Transcript ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:Exon ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -9916,79 +9920,106 @@ biolink:ExonToTranscriptRelationship a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ] ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ] ; sh:targetClass biolink:ExonToTranscriptRelationship . biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between an exposure event and an outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:subject_label_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 34 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:subject_category ], + [ sh:class biolink:Outcome ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 4 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:negated ], - [ sh:description "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:temporal_context_qualifier ], + sh:order 7 ; + sh:path biolink:qualifiers ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 29 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:class biolink:Outcome ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 4 ; - sh:path rdf:object ], + sh:order 30 ; + sh:path biolink:p_value ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -9996,90 +10027,34 @@ biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:population_context_qualifier ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:p_value ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:description "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 1 ; + sh:path biolink:temporal_context_qualifier ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -10087,98 +10062,135 @@ biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:population_context_qualifier ], + sh:order 33 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:subject_namespace ], + sh:order 6 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:object_closure ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 26 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 39 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ] ; + sh:order 5 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 25 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:ExposureEventToOutcomeAssociation . biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:property [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 48 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:class biolink:ExposureEvent ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -10186,128 +10198,126 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 39 ; + sh:path biolink:has_count ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:double ; sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:order 42 ; sh:path biolink:has_percentage ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:minCount 1 ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 36 ; sh:path dct:description ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 45 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:order 47 ; sh:path biolink:qualified_predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:order 40 ; sh:path biolink:has_total ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 43 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:order 41 ; sh:path biolink:has_quotient ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 46 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -10320,81 +10330,73 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:has_count ], + sh:order 14 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ] ; + sh:order 44 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ] ; sh:targetClass biolink:ExposureEventToPhenotypicFeatureAssociation . biolink:FeatureOrDiseaseQualifiersToEntityMixin a sh:NodeShape ; sh:closed false ; sh:description "Qualifiers for disease or phenotype to entity associations." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:property [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path rdf:object ], + sh:order 4 ; + sh:path biolink:qualified_predicate ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; @@ -10405,6 +10407,18 @@ biolink:FeatureOrDiseaseQualifiersToEntityMixin a sh:NodeShape ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path rdf:object ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 7 ; + sh:path rdf:predicate ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; @@ -10417,213 +10431,194 @@ biolink:FeatureOrDiseaseQualifiersToEntityMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path rdf:predicate ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualified_predicate ] ; + sh:path biolink:subject_aspect_qualifier ] ; sh:targetClass biolink:FeatureOrDiseaseQualifiersToEntityMixin . biolink:Food a sh:NodeShape ; sh:closed true ; sh:description "A substance consumed by a living organism as a source of nutrition" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:category ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], + [ sh:datatype xsd:string ; + sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:max_tolerated_dose ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:trade_name ], [ sh:datatype xsd:string ; sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 12 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], + sh:order 0 ; + sh:path biolink:is_supplement ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 17 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; - sh:description "" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 12 ; - sh:path biolink:synonym ], + sh:order 18 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:order 16 ; - sh:path rdf:type ] ; + sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:is_toxic ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:Food . biolink:FoodAdditive a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 5 ; sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 8 ; - sh:path biolink:synonym ], + sh:order 2 ; + sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:id ], + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:is_toxic ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:full_name ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_chemical_role ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; sh:order 0 ; - sh:path biolink:trade_name ] ; + sh:path biolink:trade_name ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ] ; sh:targetClass biolink:FoodAdditive . biolink:FrequencyQualifierMixin a sh:NodeShape ; sh:closed false ; sh:description "Qualifier for frequency type associations" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; @@ -10634,6 +10629,11 @@ biolink:FrequencyQualifierMixin a sh:NodeShape ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:frequency_qualifier ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -10651,16 +10651,16 @@ biolink:FrequencyQuantifier a sh:NodeShape ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:has_total ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:has_percentage ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:has_count ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:order 2 ; @@ -10671,150 +10671,119 @@ biolink:FunctionalAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "class describing the activity, process or localization of the gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 34 ; + sh:path rdfs:label ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:deprecated ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -10822,27 +10791,41 @@ biolink:FunctionalAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OntologyClass ; + sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -10850,11 +10833,28 @@ biolink:FunctionalAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 33 ; @@ -10868,33 +10868,14 @@ biolink:Fungus a sh:NodeShape ; sh:property [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; @@ -10904,78 +10885,102 @@ biolink:Fungus a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ] ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ] ; sh:targetClass biolink:Fungus . biolink:GeneAffectsChemicalAssociation a sh:NodeShape ; sh:closed true ; sh:description "Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 41 ; - sh:path biolink:subject_label_closure ], + sh:order 44 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 42 ; - sh:path biolink:object_label_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_direction_qualifier ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 41 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 35 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; + sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:subject_namespace ], + sh:order 12 ; + sh:path biolink:causal_mechanism_qualifier ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:timepoint ], + [ sh:class biolink:AnatomicalEntity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:subject_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 42 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:object_category_closure ], + sh:order 21 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:subject_category ], [ sh:class biolink:ChemicalEntity ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -10983,125 +10988,86 @@ biolink:GeneAffectsChemicalAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path rdf:object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 28 ; - sh:path biolink:agent_type ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:species_context_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 36 ; + sh:path biolink:object_closure ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], + sh:order 1 ; + sh:path biolink:subject_part_qualifier ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 50 ; + sh:path rdfs:label ], + [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; + sh:in ( "metabolite" ) ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:object_derivative_qualifier ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 48 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 49 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 19 ; sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 40 ; sh:path biolink:object_namespace ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 51 ; - sh:path dct:description ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:object_context_qualifier ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:p_value ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:object_form_or_variant_qualifier ], + sh:order 22 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:qualified_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:qualifiers ], [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:publications ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 50 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 26 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:object_category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:anatomical_context_qualifier ], + sh:order 7 ; + sh:path biolink:object_part_qualifier ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 52 ; sh:path biolink:has_attribute ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:causal_mechanism_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 36 ; - sh:path biolink:object_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 43 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:qualifier ], + sh:order 51 ; + sh:path dct:description ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -11109,356 +11075,384 @@ biolink:GeneAffectsChemicalAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 27 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:subject_category_closure ], + sh:order 23 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:AnatomicalEntity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:object_context_qualifier ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 45 ; sh:path biolink:adjusted_p_value ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 48 ; - sh:path biolink:category ], - [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; - sh:in ( "metabolite" ) ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:object_derivative_qualifier ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:object_part_qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:iri ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:primary_knowledge_source ], [ sh:class biolink:AnatomicalEntity ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:subject_context_qualifier ], + sh:order 13 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 43 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:species_context_qualifier ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 16 ; + sh:path rdf:subject ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], + sh:order 6 ; + sh:path biolink:object_form_or_variant_qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 46 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 26 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 53 ; - sh:path biolink:deprecated ], + sh:order 5 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 25 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:subject_derivative_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:original_object ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 31 ; + sh:path biolink:original_predicate ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 16 ; - sh:path rdf:subject ], + sh:order 28 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:object_category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 47 ; + sh:path biolink:iri ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 49 ; - sh:path rdf:type ] ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 46 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 53 ; + sh:path biolink:deprecated ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 17 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:GeneAffectsChemicalAssociation . biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:p_value ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path dct:description ], + sh:order 25 ; + sh:path biolink:object_category_closure ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 35 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 15 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 40 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], + sh:order 18 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 19 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_total ], + sh:order 31 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 33 ; sh:path biolink:id ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], + sh:order 41 ; + sh:path biolink:has_count ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 34 ; + sh:path biolink:iri ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_count ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], + sh:order 48 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 36 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], [ sh:description "The relationship to the disease" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 44 ; + sh:path biolink:has_percentage ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:iri ], + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 47 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 27 ; sh:path biolink:object_namespace ], - [ sh:description "a point in time" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ] ; + sh:order 38 ; + sh:path dct:description ] ; sh:targetClass biolink:GeneAsAModelOfDiseaseAssociation . biolink:GeneExpressionMixin a sh:NodeShape ; sh:closed false ; sh:description "Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], - [ sh:class biolink:LifeStage ; + sh:property [ sh:class biolink:LifeStage ; sh:description "stage during which gene or protein expression of takes place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; @@ -11470,6 +11464,12 @@ biolink:GeneExpressionMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:quantifier_qualifier ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:expression_site ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; sh:maxCount 1 ; @@ -11492,39 +11492,13 @@ biolink:GeneGroupingMixin a sh:NodeShape ; biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 38 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; sh:maxCount 1 ; @@ -11532,126 +11506,159 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 1 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 4 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:order 43 ; + sh:path biolink:has_total ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 19 ; sh:path biolink:original_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:description "a human-readable description of an entity" ; + sh:order 20 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path dct:description ], + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_count ], + sh:order 48 ; + sh:path biolink:qualified_predicate ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 17 ; sh:path biolink:timepoint ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:original_object ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 36 ; - sh:path biolink:category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 35 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 37 ; - sh:path rdf:type ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_total ], + sh:order 45 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:knowledge_source ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], + sh:order 26 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:negated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 36 ; + sh:path biolink:category ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 34 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:object_direction_qualifier ], + sh:order 44 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_subject ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:sex_qualifier ], + sh:order 38 ; + sh:path rdfs:label ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -11659,138 +11666,128 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 16 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 37 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:iri ], + sh:order 40 ; + sh:path biolink:has_attribute ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 29 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:double ; + sh:order 18 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_quotient ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 42 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 24 ; - sh:path biolink:object_closure ] ; + sh:path biolink:object_closure ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 34 ; + sh:path biolink:id ] ; sh:targetClass biolink:GeneHasVariantThatContributesToDiseaseAssociation . biolink:GeneProductIsoformMixin a sh:NodeShape ; sh:closed false ; sh:description "This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:order 2 ; sh:path rdfs:label ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ] ; + sh:path biolink:xref ] ; sh:targetClass biolink:GeneProductIsoformMixin . biolink:GeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 40 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ], + sh:order 6 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 28 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], + sh:order 18 ; + sh:path biolink:original_predicate ], [ sh:class biolink:Disease ; sh:description "disease" ; sh:maxCount 1 ; @@ -11798,42 +11795,86 @@ biolink:GeneToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 48 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 33 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], + sh:order 39 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:order 43 ; sh:path biolink:has_quotient ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_percentage ], + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; @@ -11844,105 +11885,47 @@ biolink:GeneToDiseaseAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 27 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:description "a point in time" ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 35 ; sh:path biolink:category ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:has_total ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:deprecated ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 38 ; sh:path dct:description ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], + sh:order 5 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:object_label_closure ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -11950,226 +11933,130 @@ biolink:GeneToDiseaseAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 15 ; sh:path biolink:agent_type ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model" ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ] ; - sh:targetClass biolink:GeneToDiseaseAssociation . - -biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 14 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 36 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:deprecated ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], + sh:order 25 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:minCount 1 ; sh:order 3 ; - sh:path rdf:predicate ], + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:double ; sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:order 44 ; sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_quotient ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 47 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the phenotypic feature" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:subject ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], + sh:order 21 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 19 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], + sh:order 34 ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:order 26 ; + sh:path biolink:subject_namespace ] ; + sh:targetClass biolink:GeneToDiseaseAssociation . + +biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:p_value ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:iri ], + sh:order 38 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 33 ; sh:path biolink:id ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -12177,53 +12064,176 @@ biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 15 ; sh:path biolink:agent_type ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path dct:description ], + sh:order 40 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 39 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], + sh:order 5 ; + sh:path biolink:sex_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:iri ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 44 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 35 ; + sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 17 ; sh:path biolink:original_subject ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:has_total ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], + sh:order 4 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 47 ; + sh:path biolink:qualified_predicate ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 48 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 26 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the phenotypic feature" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:subject ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:has_quotient ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; @@ -12234,33 +12244,21 @@ biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_count ] ; + sh:order 7 ; + sh:path biolink:qualifier ] ; sh:targetClass biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . biolink:GeneToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene that is the subject of the association" ; + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -12268,345 +12266,342 @@ biolink:GeneToEntityAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ] ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:GeneToEntityAssociationMixin . biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 37 ; + sh:path dct:description ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:subject_closure ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 35 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:object_closure ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which the gene is expressed" ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], + sh:order 30 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "can be used to indicate magnitude, or also ranking" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:quantifier_qualifier ], + sh:minCount 1 ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 25 ; sh:path biolink:subject_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:p_value ], + sh:order 31 ; + sh:path biolink:adjusted_p_value ], [ sh:description "expression relationship" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path rdf:predicate ], - [ sh:description "a point in time" ; + [ sh:class biolink:LifeStage ; + sh:description "stage at which the gene is expressed in the site" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], + sh:order 0 ; + sh:path biolink:stage_qualifier ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 18 ; sh:path biolink:original_object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:order 39 ; + sh:path biolink:deprecated ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:object_namespace ], + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], + sh:order 19 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "can be used to indicate magnitude, or also ranking" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 1 ; + sh:path biolink:quantifier_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 32 ; - sh:path biolink:id ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 34 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], - [ sh:class biolink:LifeStage ; - sh:description "stage at which the gene is expressed in the site" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:stage_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:negated ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location." ; + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which the gene is expressed" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 4 ; + sh:path rdf:object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ] ; + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:knowledge_source ] ; sh:targetClass biolink:GeneToExpressionSiteAssociation . biolink:GeneToGeneAssociation a sh:NodeShape ; sh:closed false ; sh:description "abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; + sh:property [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 33 ; sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -12617,402 +12612,302 @@ biolink:GeneToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ] ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ] ; sh:targetClass biolink:GeneToGeneAssociation . biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; sh:closed true ; sh:description "Indicates that two genes are co-expressed, generally under the same conditions." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 36 ; - sh:path biolink:category ], + sh:property [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:timepoint ], [ sh:class biolink:LifeStage ; sh:description "stage during which gene or protein expression of takes place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:stage_qualifier ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], + sh:order 7 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "Optional quantitative value indicating degree of expression." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:quantifier_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 37 ; - sh:path rdf:type ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path dct:description ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 34 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 4 ; - sh:path rdf:subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_predicate ], + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 32 ; sh:path biolink:p_value ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 6 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 6 ; + sh:path rdf:object ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], + sh:minCount 1 ; + sh:order 5 ; + sh:path rdf:predicate ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 41 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 27 ; sh:path biolink:subject_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:description "a point in time" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 39 ; + sh:path dct:description ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path biolink:original_predicate ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 5 ; - sh:path rdf:predicate ], + sh:order 15 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 18 ; sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 34 ; - sh:path biolink:id ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 37 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:phenotypic_state ], + sh:order 10 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 38 ; sh:path rdfs:label ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ] ; - sh:targetClass biolink:GeneToGeneCoexpressionAssociation . - -biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 20 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 24 ; + sh:order 28 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 4 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:expression_site ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 5 ; + sh:order 9 ; sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:phenotypic_state ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; + sh:order 30 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:iri ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 7 ; + sh:order 11 ; sh:path biolink:has_evidence ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 36 ; + sh:path biolink:category ] ; + sh:targetClass biolink:GeneToGeneCoexpressionAssociation . + +biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; @@ -13022,110 +12917,150 @@ biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:class biolink:GeneFamily ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:description "membership of the gene in the given gene family." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ] ; - sh:targetClass biolink:GeneToGeneFamilyAssociation . - -biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:GeneFamily ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; + sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -13133,59 +13068,39 @@ biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:primary_knowledge_source ] ; + sh:targetClass biolink:GeneToGeneFamilyAssociation . + +biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; @@ -13195,115 +13110,164 @@ biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:description "homology relationship type" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:GeneToGeneHomologyAssociation . - -biolink:GeneToGeneProductRelationship a sh:NodeShape ; - sh:closed true ; - sh:description "A gene is transcribed and potentially translated to a gene product" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -13311,66 +13275,66 @@ biolink:GeneToGeneProductRelationship a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 34 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:GeneToGeneHomologyAssociation . + +biolink:GeneToGeneProductRelationship a sh:NodeShape ; + sh:closed true ; + sh:description "A gene is transcribed and potentially translated to a gene product" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:GeneProductMixin ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 23 ; sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 34 ; + sh:path rdfs:label ], [ sh:class biolink:Gene ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -13378,790 +13342,831 @@ biolink:GeneToGeneProductRelationship a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:GeneProductMixin ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:iri ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; - sh:path biolink:object_label_closure ] ; - sh:targetClass biolink:GeneToGeneProductRelationship . - -biolink:GeneToGoTermAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Publication ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "class describing the activity, process or localization of the gene product" ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Gene ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 36 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:GeneToGeneProductRelationship . + +biolink:GeneToGoTermAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ] ; - sh:targetClass biolink:GeneToGoTermAssociation . - -biolink:GeneToPathwayAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An interaction between a gene or gene product and a biological process or pathway." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 35 ; + sh:path dct:description ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Gene ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "a human-readable description of an entity" ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the gene or gene product entity that participates or influences the pathway" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:class biolink:Pathway ; - sh:description "the pathway that includes or is affected by the gene or gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 33 ; sh:path rdf:type ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 30 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ] ; + sh:targetClass biolink:GeneToGoTermAssociation . + +biolink:GeneToPathwayAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An interaction between a gene or gene product and a biological process or pathway." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Pathway ; + sh:description "the pathway that includes or is affected by the gene or gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:deprecated ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the gene or gene product entity that participates or influences the pathway" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ] ; - sh:targetClass biolink:GeneToPathwayAssociation . - -biolink:GeneToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:iri ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 6 ; + sh:order 3 ; sh:path biolink:negated ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 34 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; + sh:order 12 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_total ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 17 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:order 31 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 11 ; + sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the phenotypic feature" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 26 ; + sh:order 23 ; sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; + sh:order 18 ; sh:path biolink:object_category ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ] ; + sh:targetClass biolink:GeneToPathwayAssociation . + +biolink:GeneToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 19 ; sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_quotient ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_percentage ], + sh:minCount 1 ; + sh:order 33 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:subject_category_closure ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 48 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 28 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_count ], + sh:order 43 ; + sh:path biolink:has_quotient ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:object_direction_qualifier ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path dct:description ], + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 40 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 47 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:sex_qualifier ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:GeneToPhenotypicFeatureAssociation . - -biolink:Genome a sh:NodeShape ; - sh:closed true ; - sh:description "A genome is the sum of genetic material within a cell or virion." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 27 ; + sh:path biolink:object_namespace ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 11 ; + sh:order 37 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], + sh:order 6 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:has_count ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:has_total ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 44 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the phenotypic feature" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 35 ; + sh:path biolink:category ] ; + sh:targetClass biolink:GeneToPhenotypicFeatureAssociation . + +biolink:Genome a sh:NodeShape ; + sh:closed true ; + sh:description "A genome is the sum of genetic material within a cell or virion." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:order 10 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:has_biological_sequence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path biolink:category ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path rdfs:label ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 8 ; @@ -14169,325 +14174,173 @@ biolink:Genome a sh:NodeShape ; [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ] ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:Genome . biolink:GenomicBackgroundExposure a sh:NodeShape ; sh:closed true ; sh:description "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:has_attribute ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 6 ; + sh:path rdfs:label ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 8 ; + sh:path biolink:has_quantitative_value ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_gene_or_gene_product ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 12 ; - sh:path biolink:xref ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:deprecated ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:string ; - sh:order 16 ; - sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 12 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 11 ; sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:category ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:QuantityValue ; + [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 8 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 14 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:GenomicBackgroundExposure . - -biolink:GenomicEntity a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ] ; - sh:targetClass biolink:GenomicEntity . - -biolink:GenomicSequenceLocalization a sh:NodeShape ; - sh:closed true ; - sh:description "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_source ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; sh:order 9 ; - sh:path biolink:qualifier ], + sh:path biolink:has_qualitative_value ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:subject_namespace ], + sh:order 7 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 15 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens." ; - sh:in ( "+" "-" "." "?" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:genome_build ], - [ sh:description "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." ; - sh:in ( "0" "1" "2" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:phase ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 6 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:integer ; - sh:description "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:end_interbase_coordinate ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 15 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:original_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 19 ; + sh:path biolink:deprecated ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:order 17 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:integer ; - sh:description "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0)." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:start_interbase_coordinate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:knowledge_level ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path rdf:object ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 37 ; - sh:path biolink:category ], + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 35 ; + sh:order 5 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:qualifiers ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 1 ; + sh:path biolink:has_gene_or_gene_product ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path biolink:full_name ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:in_taxon_label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 14 ; + sh:path biolink:synonym ], [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:timepoint ], + sh:order 0 ; + sh:path biolink:timepoint ] ; + sh:targetClass biolink:GenomicBackgroundExposure . + +biolink:GenomicEntity a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ] ; + sh:targetClass biolink:GenomicEntity . + +biolink:GenomicSequenceLocalization a sh:NodeShape ; + sh:closed true ; + sh:description "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 33 ; sh:path biolink:p_value ], - [ sh:description "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)." ; - sh:in ( "+" "-" "." "?" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:strand ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 31 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 38 ; sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 16 ; + sh:path biolink:knowledge_level ], + [ sh:description "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens." ; + sh:in ( "+" "-" "." "?" ) ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:primary_knowledge_source ], + sh:order 2 ; + sh:path biolink:genome_build ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_subject ], + sh:order 8 ; + sh:path biolink:negated ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 24 ; sh:path biolink:subject_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -14497,277 +14350,396 @@ biolink:GenomicSequenceLocalization a sh:NodeShape ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 21 ; - sh:path biolink:original_object ] ; - sh:targetClass biolink:GenomicSequenceLocalization . - -biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 34 ; + sh:path biolink:adjusted_p_value ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 34 ; + sh:order 39 ; sh:path rdfs:label ], - [ sh:class biolink:Genotype ; - sh:description "A genotype that has a role in modeling the disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:publications ], + [ sh:datatype xsd:integer ; + sh:description "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0)." ; + sh:maxCount 1 ; sh:order 0 ; - sh:path rdf:subject ], + sh:path biolink:start_interbase_coordinate ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; + sh:order 35 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 40 ; + sh:path dct:description ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_source ], + [ sh:description "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." ; + sh:in ( "0" "1" "2" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:phase ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 27 ; + sh:order 32 ; sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 28 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 15 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:integer ; + sh:description "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 1 ; + sh:path biolink:end_interbase_coordinate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; + sh:order 22 ; sh:path biolink:subject_category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:iri ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path biolink:original_subject ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path rdf:object ], + [ sh:description "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)." ; + sh:in ( "+" "-" "." "?" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:strand ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 37 ; + sh:path biolink:category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 41 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 42 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:GenomicSequenceLocalization . + +biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_direction_qualifier ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "The relationship to the disease" ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:object_direction_qualifier ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 34 ; + sh:path rdfs:label ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:order 40 ; sh:path biolink:object_aspect_qualifier ], - [ sh:description "a point in time" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:frequency_qualifier ], + sh:order 39 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:description "The relationship to the disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Genotype ; + sh:description "A genotype that has a role in modeling the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 33 ; sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 38 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ] ; - sh:targetClass biolink:GenotypeAsAModelOfDiseaseAssociation . - -biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:object_aspect_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_direction_qualifier ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ] ; + sh:targetClass biolink:GenotypeAsAModelOfDiseaseAssociation . + +biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:qualified_predicate ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:Disease ; sh:description "a disease that is associated with that genotype" ; sh:maxCount 1 ; @@ -14775,362 +14747,301 @@ biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 39 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Genotype ; - sh:description "a genotype that is associated in some way with a disease state" ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:description "E.g. is pathogenic for" ; + sh:order 41 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:qualified_predicate ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 34 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 43 ; sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:deprecated ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:order 38 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:class biolink:Genotype ; + sh:description "a genotype that is associated in some way with a disease state" ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:subject_direction_qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; - sh:path biolink:has_evidence ] ; - sh:targetClass biolink:GenotypeToDiseaseAssociation . - -biolink:GenotypeToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:path biolink:has_evidence ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:Genotype ; - sh:description "genotype that is the subject of the association" ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; - sh:targetClass biolink:GenotypeToEntityAssociationMixin . - -biolink:GenotypeToGeneAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 33 ; sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "E.g. is pathogenic for" ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 30 ; sh:path biolink:id ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Genotype ; - sh:description "parent genotype" ; + sh:path biolink:qualifier ] ; + sh:targetClass biolink:GenotypeToDiseaseAssociation . + +biolink:GenotypeToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Genotype ; + sh:description "genotype that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:defaultValue "not_provided" ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; + sh:targetClass biolink:GenotypeToEntityAssociationMixin . + +biolink:GenotypeToGeneAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:description "the relationship type used to connect genotype to gene" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:Gene ; sh:description "gene implicated in genotype" ; sh:maxCount 1 ; @@ -15138,82 +15049,143 @@ biolink:GenotypeToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "the relationship type used to connect genotype to gene" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ] ; - sh:targetClass biolink:GenotypeToGeneAssociation . - -biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Any association between one genotype and a genotypic entity that is a sub-component of it" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Genotype ; + sh:description "parent genotype" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:description "a point in time" ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 35 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ] ; + sh:targetClass biolink:GenotypeToGeneAssociation . + +biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Any association between one genotype and a genotypic entity that is a sub-component of it" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Genotype ; + sh:description "child genotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:Genotype ; sh:description "parent genotype" ; sh:maxCount 1 ; @@ -15221,42 +15193,34 @@ biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 34 ; sh:path rdfs:label ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -15264,74 +15228,120 @@ biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:Genotype ; - sh:description "child genotype" ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -15339,39 +15349,26 @@ biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ] ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ] ; sh:targetClass biolink:GenotypeToGenotypePartAssociation . biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -15379,36 +15376,55 @@ biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 18 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], + sh:order 45 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 40 ; + sh:path biolink:has_total ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -15416,239 +15432,269 @@ biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:order 41 ; sh:path biolink:has_quotient ], - [ sh:class biolink:Genotype ; - sh:description "genotype that is associated with the phenotypic feature" ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 17 ; sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 48 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 29 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 43 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:has_count ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:Genotype ; + sh:description "genotype that is associated with the phenotypic feature" ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 33 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:subject_namespace ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 12 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 47 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 44 ; + sh:path biolink:subject_direction_qualifier ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 46 ; sh:path biolink:object_direction_qualifier ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], + sh:order 39 ; + sh:path biolink:has_count ] ; + sh:targetClass biolink:GenotypeToPhenotypicFeatureAssociation . + +biolink:GenotypeToVariantAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Any association between a genotype and a sequence variant." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:description "the relationship type used to connect genotype to gene" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 10 ; + sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ] ; - sh:targetClass biolink:GenotypeToPhenotypicFeatureAssociation . - -biolink:GenotypeToVariantAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Any association between a genotype and a sequence variant." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:description "the relationship type used to connect genotype to gene" ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; @@ -15656,8 +15702,23 @@ biolink:GenotypeToVariantAssociation a sh:NodeShape ; [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:class biolink:SequenceVariant ; + sh:description "gene implicated in genotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], [ sh:class biolink:Genotype ; sh:description "parent genotype" ; sh:maxCount 1 ; @@ -15665,227 +15726,185 @@ biolink:GenotypeToVariantAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:SequenceVariant ; - sh:description "gene implicated in genotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 30 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 34 ; sh:path rdfs:label ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 29 ; - sh:path biolink:adjusted_p_value ] ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:GenotypeToVariantAssociation . biolink:GenotypicSex a sh:NodeShape ; sh:closed true ; sh:description "An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 10 ; sh:path biolink:category ], - [ sh:class biolink:NamedThing ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:order 4 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:order 11 ; sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 12 ; sh:path dct:description ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 0 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ] ; + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:GenotypicSex . biolink:GeographicExposure a sh:NodeShape ; sh:closed true ; sh:description "A geographic exposure is a factor relating to geographic proximity to some impactful entity." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:timepoint ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 10 ; sh:path biolink:synonym ], @@ -15893,12 +15912,6 @@ biolink:GeographicExposure a sh:NodeShape ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 7 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -15906,151 +15919,138 @@ biolink:GeographicExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 13 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ] ; + sh:path dct:description ] ; sh:targetClass biolink:GeographicExposure . biolink:GeographicLocation a sh:NodeShape ; sh:closed true ; sh:description "a location that can be described in lat/long coordinates" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:float ; + sh:description "latitude" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:latitude ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:float ; - sh:description "latitude" ; + sh:description "longitude" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:latitude ], + sh:order 1 ; + sh:path biolink:longitude ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:datatype xsd:float ; - sh:description "longitude" ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:longitude ] ; + sh:order 11 ; + sh:path dct:description ] ; sh:targetClass biolink:GeographicLocation . biolink:GeographicLocationAtTime a sh:NodeShape ; sh:closed true ; sh:description "a location that can be described in lat/long coordinates, for a particular time" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 7 ; sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:float ; + sh:description "longitude" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:longitude ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 9 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 4 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 3 ; @@ -16060,211 +16060,211 @@ biolink:GeographicLocationAtTime a sh:NodeShape ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:latitude ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 6 ; - sh:path biolink:synonym ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path rdfs:label ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 12 ; sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "longitude" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:longitude ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ] ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 6 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:GeographicLocationAtTime . biolink:GrossAnatomicalStructure a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ] ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:GrossAnatomicalStructure . biolink:Haplotype a sh:NodeShape ; sh:closed true ; sh:description "A set of zero or more Alleles on a single instance of a Sequence[VMC]" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "connects a genomic feature to its sequence" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:id ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 11 ; sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], + sh:order 0 ; + sh:path biolink:has_biological_sequence ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 8 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ] ; + sh:path biolink:iri ] ; sh:targetClass biolink:Haplotype . biolink:Hospitalization a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; sh:path biolink:provided_by ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ] ; + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path dct:description ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ] ; sh:targetClass biolink:Hospitalization . biolink:HospitalizationOutcome a sh:NodeShape ; @@ -16277,13 +16277,13 @@ biolink:Human a sh:NodeShape ; sh:closed true ; sh:description "A member of the the species Homo sapiens." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; @@ -16293,87 +16293,118 @@ biolink:Human a sh:NodeShape ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ] ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ] ; sh:targetClass biolink:Human . biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:closed true ; sh:description "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 25 ; sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -16381,150 +16412,119 @@ biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:iri ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a human-readable description of an entity" ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:deprecated ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 33 ; @@ -16545,288 +16545,291 @@ biolink:Invertebrate a sh:NodeShape ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ] ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ] ; sh:targetClass biolink:Invertebrate . biolink:JournalArticle a sh:NodeShape ; sh:closed true ; sh:description "an article, typically presenting results of research, that is published in an issue of a scientific journal." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:creation_date ], + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 17 ; + sh:path biolink:synonym ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:authors ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 8 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:license ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path dct:description ], + sh:order 12 ; + sh:path biolink:rights ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 20 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:summary ], - [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + [ sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 18 ; - sh:path biolink:id ], + sh:order 0 ; + sh:path biolink:published_in ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 9 ; + sh:path biolink:xref ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:rights ], + sh:order 11 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:volume ], + sh:order 3 ; + sh:path biolink:issue ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 25 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:iso_abbreviation ], [ sh:datatype xsd:string ; sh:order 21 ; sh:path rdf:type ], - [ sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:published_in ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 9 ; - sh:path biolink:xref ], + sh:order 14 ; + sh:path biolink:creation_date ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; sh:order 10 ; sh:path dct:type ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 15 ; - sh:path biolink:provided_by ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 22 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 17 ; - sh:path biolink:synonym ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:authors ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:full_name ], + sh:order 6 ; + sh:path biolink:summary ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:has_attribute ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 8 ; - sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; + sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:issue ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 1 ; + sh:path biolink:iso_abbreviation ], + [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 18 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:order 5 ; sh:path biolink:pages ], + [ sh:datatype xsd:string ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:volume ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:format ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "keywords tagging a publication" ; sh:order 7 ; - sh:path biolink:keywords ] ; + sh:path biolink:keywords ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 15 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:JournalArticle . biolink:LogOddsAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a log odds ratio analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:creation_date ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 12 ; + sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:rights ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:order 11 ; sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ] ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ] ; sh:targetClass biolink:LogOddsAnalysisResult . biolink:MacromolecularComplex a sh:NodeShape ; sh:closed true ; sh:description "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:full_name ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 7 ; sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 4 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:order 10 ; sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 6 ; + sh:path biolink:synonym ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:order 0 ; @@ -16835,234 +16838,242 @@ biolink:MacromolecularComplex a sh:NodeShape ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 3 ; sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ] ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:MacromolecularComplex . biolink:MacromolecularMachineToBiologicalProcessAssociation a sh:NodeShape ; sh:closed true ; sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:property [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:BiologicalProcess ; - sh:description "class describing the activity, process or localization of the gene product" ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:object_namespace ], + [ sh:class biolink:BiologicalProcess ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 31 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 25 ; sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_attribute ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; - sh:path biolink:agent_type ] ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ] ; sh:targetClass biolink:MacromolecularMachineToBiologicalProcessAssociation . biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:closed true ; sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 32 ; sh:path biolink:category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -17070,43 +17081,23 @@ biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 33 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 31 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:MacromolecularMachineMixin ; sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; @@ -17114,62 +17105,46 @@ biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_subject ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -17177,75 +17152,102 @@ biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:order 18 ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:CellularComponent ; + sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 30 ; sh:path biolink:id ], - [ sh:class biolink:CellularComponent ; - sh:description "class describing the activity, process or localization of the gene product" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ] ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ] ; sh:targetClass biolink:MacromolecularMachineToCellularComponentAssociation . biolink:MacromolecularMachineToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "an association which has a macromolecular machine mixin as a subject" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -17253,45 +17255,18 @@ biolink:MacromolecularMachineToEntityAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; + sh:order 1 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:MacromolecularMachineToEntityAssociationMixin . biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; sh:closed true ; sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:original_predicate ], @@ -17300,10 +17275,37 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:MolecularActivity ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; @@ -17313,72 +17315,32 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; sh:order 25 ; sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 35 ; sh:path dct:description ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:class biolink:MacromolecularMachineMixin ; sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; @@ -17386,96 +17348,124 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 30 ; sh:path biolink:id ], - [ sh:class biolink:MolecularActivity ; - sh:description "class describing the activity, process or localization of the gene product" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "a point in time" ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ] ; + sh:order 14 ; + sh:path biolink:original_subject ] ; sh:targetClass biolink:MacromolecularMachineToMolecularActivityAssociation . biolink:Mammal a sh:NodeShape ; sh:closed true ; sh:description "A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the possession of hair, three middle ear bones, mammary glands, and a neocortex" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; @@ -17484,40 +17474,50 @@ biolink:Mammal a sh:NodeShape ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ] ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ] ; sh:targetClass biolink:Mammal . biolink:MappingCollection a sh:NodeShape ; @@ -17535,119 +17535,38 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a material sample and the material entity from which it is derived." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "derivation relationship" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 35 ; sh:path dct:description ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:MaterialSample ; - sh:description "the material sample being described" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "derivation relationship" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -17655,39 +17574,41 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:NamedThing ; - sh:description "the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + sh:order 30 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:NamedThing ; + sh:description "the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; @@ -17699,242 +17620,321 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:MaterialSample ; + sh:description "the material sample being described" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ] ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ] ; sh:targetClass biolink:MaterialSampleDerivationAssociation . biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a material sample and a disease or phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:property [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 34 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:MaterialSample ; - sh:description "the material sample being described" ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 35 ; sh:path dct:description ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 31 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:MaterialSample ; + sh:description "the material sample being described" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ] ; + sh:order 16 ; + sh:path biolink:original_object ] ; sh:targetClass biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . biolink:MaterialSampleToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "An association between a material sample and something." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:class biolink:MaterialSample ; sh:description "the material sample being described" ; sh:maxCount 1 ; @@ -17947,64 +17947,64 @@ biolink:MaterialSampleToEntityAssociationMixin a sh:NodeShape ; biolink:MicroRNA a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 0 ; sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:full_name ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ] ; + sh:order 11 ; + sh:path dct:description ] ; sh:targetClass biolink:MicroRNA . biolink:ModelToDiseaseAssociationMixin a sh:NodeShape ; @@ -18037,105 +18037,95 @@ biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 32 ; sh:path biolink:category ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], [ sh:class biolink:MolecularActivity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -18143,170 +18133,248 @@ biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ] ; + sh:targetClass biolink:MolecularActivityToChemicalEntityAssociation . + +biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; - sh:targetClass biolink:MolecularActivityToChemicalEntityAssociation . - -biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -18314,6 +18382,17 @@ biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], + [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 34 ; @@ -18322,37 +18401,11 @@ biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:class biolink:MolecularActivity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -18360,59 +18413,6 @@ biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; @@ -18424,131 +18424,87 @@ biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; sh:closed true ; sh:description "Association that holds the relationship between a reaction and the pathway it participates in." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:defaultValue "not_provided" ; + sh:property [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:class biolink:Pathway ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:class biolink:Pathway ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -18556,160 +18512,204 @@ biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 31 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; - sh:path biolink:qualifiers ] ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ] ; sh:targetClass biolink:MolecularActivityToPathwayAssociation . biolink:MolecularMixture a sh:NodeShape ; sh:closed true ; sh:description "A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:order 16 ; + sh:path rdf:type ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 12 ; sh:path biolink:synonym ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:full_name ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:trade_name ], [ sh:datatype xsd:string ; - sh:order 16 ; - sh:path rdf:type ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; - sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:max_tolerated_dose ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:iri ], + sh:order 7 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], + sh:order 20 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:is_supplement ], + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 18 ; sh:path dct:description ], - [ sh:datatype xsd:boolean ; + [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ] ; + sh:order 0 ; + sh:path biolink:is_supplement ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ] ; sh:targetClass biolink:MolecularMixture . biolink:MortalityOutcome a sh:NodeShape ; @@ -18722,56 +18722,42 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape sh:closed true ; sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 15 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 38 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:qualifier ], + sh:order 7 ; + sh:path biolink:population_context_qualifier ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:original_object ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 37 ; sh:path biolink:category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:publications ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:p_value ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -18781,391 +18767,393 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 30 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:original_object ], + sh:order 23 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 9 ; + sh:path biolink:qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; + sh:order 12 ; + sh:path biolink:has_evidence ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:population_context_qualifier ], + sh:order 39 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 35 ; sh:path biolink:id ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:object_context_qualifier ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 15 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 40 ; + sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:negated ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 5 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:knowledge_level ], + sh:order 36 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:primary_knowledge_source ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 38 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 18 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:p_value ], + sh:order 20 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], + sh:order 6 ; + sh:path biolink:object_context_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 31 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:subject_closure ], + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:object_namespace ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:original_subject ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path dct:description ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:subject_context_qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence ] ; + sh:order 4 ; + sh:path rdf:object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_aspect_qualifier ] ; sh:targetClass biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . biolink:NoncodingRNAProduct a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], + sh:property [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:full_name ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ] ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ] ; sh:targetClass biolink:NoncodingRNAProduct . biolink:NucleicAcidSequenceMotif a sh:NodeShape ; sh:closed true ; sh:description "A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 8 ; + sh:path biolink:category ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ] ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:NucleicAcidSequenceMotif . biolink:NucleosomeModification a sh:NodeShape ; sh:closed true ; sh:description "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; sh:order 6 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 3 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:deprecated ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:order 11 ; sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 9 ; sh:path biolink:category ], - [ sh:description "connects a genomic feature to its sequence" ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ] ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:iri ] ; sh:targetClass biolink:NucleosomeModification . biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a observed expected frequency analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], + sh:order 2 ; + sh:path biolink:format ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:order 11 ; sh:path rdf:type ], @@ -19173,36 +19161,48 @@ biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; sh:maxCount 1 ; sh:order 12 ; sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ] ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:ObservedExpectedFrequencyAnalysisResult . biolink:Occurrent a sh:NodeShape ; @@ -19215,49 +19215,39 @@ biolink:OrganismAttribute a sh:NodeShape ; sh:closed true ; sh:description "describes a characteristic of an organismal entity." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 0 ; sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -19265,19 +19255,29 @@ biolink:OrganismAttribute a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:order 11 ; sh:path rdf:type ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 12 ; @@ -19288,13 +19288,11 @@ biolink:OrganismTaxonToEntityAssociation a sh:NodeShape ; sh:closed false ; sh:description "An association between an organism taxon and another entity" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "organism taxon that is the subject of the association" ; + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -19302,81 +19300,50 @@ biolink:OrganismTaxonToEntityAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:OrganismTaxon ; + sh:description "organism taxon that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ] ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:OrganismTaxonToEntityAssociation . biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the taxon that is the subject of the association" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:class biolink:NamedThing ; sh:description "the environment in which the organism occurs" ; sh:maxCount 1 ; @@ -19385,37 +19352,35 @@ biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; sh:order 2 ; sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:description "predicate describing the relationship between the taxon and the environment" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; @@ -19425,109 +19390,85 @@ biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 35 ; + sh:path dct:description ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "predicate describing the relationship between the taxon and the environment" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ] ; - sh:targetClass biolink:OrganismTaxonToEnvironmentAssociation . - -biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; - sh:closed false ; - sh:description "A relationship between two organism taxon nodes" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:defaultValue "not_provided" ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -19538,120 +19479,113 @@ biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; sh:order 34 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], [ sh:class biolink:OrganismTaxon ; - sh:description "organism taxon that is the subject of the association" ; + sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:path rdf:subject ] ; + sh:targetClass biolink:OrganismTaxonToEnvironmentAssociation . + +biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; + sh:closed false ; + sh:description "A relationship between two organism taxon nodes" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 33 ; sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -19659,613 +19593,537 @@ biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "a point in time" ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:OrganismTaxonToOrganismTaxonAssociation . - -biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; - sh:closed true ; - sh:description "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 35 ; + sh:path dct:description ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 29 ; - sh:path biolink:p_value ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:path biolink:adjusted_p_value ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], + sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 23 ; + sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OrganismTaxon ; + sh:description "organism taxon that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:order 5 ; sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 17 ; - sh:path biolink:original_object ], + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 24 ; + sh:path biolink:object_namespace ] ; + sh:targetClass biolink:OrganismTaxonToOrganismTaxonAssociation . + +biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; + sh:closed true ; + sh:description "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:description "a point in time" ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "the environment in which the two taxa interact" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 0 ; + sh:path biolink:associated_environmental_context ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 33 ; sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the taxon that is the subject of the association" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], + sh:order 6 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 27 ; sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "the environment in which the two taxa interact" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:associated_environmental_context ], + sh:minCount 1 ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_object ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 28 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the taxon that is the subject of the association" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ] ; - sh:targetClass biolink:OrganismTaxonToOrganismTaxonInteraction . - -biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; - sh:closed true ; - sh:description "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; + [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 3 ; + sh:order 4 ; sh:path biolink:negated ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; sh:order 13 ; - sh:path biolink:timepoint ], + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; + sh:order 23 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the more specific taxon" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OrganismTaxon ; - sh:description "the more general taxon" ; + sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; + sh:order 3 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; + sh:order 12 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:OrganismTaxon ; + sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 36 ; + sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 29 ; - sh:path biolink:adjusted_p_value ] ; - sh:targetClass biolink:OrganismTaxonToOrganismTaxonSpecialization . + sh:path biolink:p_value ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:OrganismTaxonToOrganismTaxonInteraction . -biolink:OrganismToOrganismAssociation a sh:NodeShape ; +biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; sh:closed true ; + sh:description "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:deprecated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:class biolink:IndividualOrganism ; - sh:description "An association between two individual organisms." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 35 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; sh:path biolink:object_label_closure ], + [ sh:class biolink:OrganismTaxon ; + sh:description "the more specific taxon" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:IndividualOrganism ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:OrganismTaxon ; + sh:description "the more general taxon" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 2 ; + sh:path rdf:object ] ; + sh:targetClass biolink:OrganismTaxonToOrganismTaxonSpecialization . + +biolink:OrganismToOrganismAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; @@ -20276,112 +20134,127 @@ biolink:OrganismToOrganismAssociation a sh:NodeShape ; sh:order 3 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ] ; - sh:targetClass biolink:OrganismToOrganismAssociation . - -biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:IndividualOrganism ; + sh:description "An association between two individual organisms." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 35 ; sh:path dct:description ], - [ sh:class biolink:OrganismalEntity ; - sh:description "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:IndividualOrganism ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -20393,104 +20266,229 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ] ; + sh:targetClass biolink:OrganismToOrganismAssociation . + +biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:order 38 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_direction_qualifier ], + sh:order 31 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 35 ; + sh:path dct:description ], [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 43 ; sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:object_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OrganismalEntity ; + sh:description "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:subject_direction_qualifier ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:object_aspect_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:description "The relationship to the disease" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -20498,39 +20496,96 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ] ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ] ; sh:targetClass biolink:OrganismalEntityAsAModelOfDiseaseAssociation . biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; sh:closed true ; sh:description "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:description "interaction relationship type" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -20538,28 +20593,26 @@ biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "a point in time" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; @@ -20570,96 +20623,23 @@ biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:deprecated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:iri ], - [ sh:description "interaction relationship type" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; @@ -20667,31 +20647,51 @@ biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:object_closure ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; @@ -20702,19 +20702,90 @@ biolink:PairwiseMolecularInteraction a sh:NodeShape ; sh:closed true ; sh:description "An interaction at the molecular level between two physical entities" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:property [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "identifier for the interaction. This may come from an interaction database such as IMEX." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "interaction relationship type" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], + sh:order 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:MolecularEntity ; sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; @@ -20722,23 +20793,38 @@ biolink:PairwiseMolecularInteraction a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path rdf:object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], + sh:order 0 ; + sh:path biolink:interacting_molecules_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path dct:description ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 33 ; + sh:path biolink:category ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -20746,113 +20832,58 @@ biolink:PairwiseMolecularInteraction a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:knowledge_level ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "interaction relationship type" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:interacting_molecules_category ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "a point in time" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "identifier for the interaction. This may come from an interaction database such as IMEX." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:class biolink:MolecularEntity ; sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; @@ -20860,139 +20891,108 @@ biolink:PairwiseMolecularInteraction a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ] ; + sh:order 32 ; + sh:path biolink:iri ] ; sh:targetClass biolink:PairwiseMolecularInteraction . biolink:Patent a sh:NodeShape ; sh:closed true ; sh:description "a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:order 6 ; + sh:path dct:type ], + [ sh:datatype xsd:string ; sh:order 17 ; sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:category ], + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:rights ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 4 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:order 6 ; - sh:path dct:type ], + sh:order 21 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], + sh:order 7 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 13 ; + sh:path biolink:synonym ], [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:order 18 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ], + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:id ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; sh:path biolink:xref ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:license ], + sh:order 2 ; + sh:path biolink:summary ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:order 3 ; + sh:path biolink:keywords ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:format ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ] ; + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:category ] ; sh:targetClass biolink:Patent . biolink:PathognomonicityQuantifier a sh:NodeShape ; @@ -21005,54 +21005,51 @@ biolink:PathologicalAnatomicalExposure a sh:NodeShape ; sh:closed true ; sh:description "An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "a point in time" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -21065,17 +21062,20 @@ biolink:PathologicalAnatomicalExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 9 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ] ; + sh:path biolink:full_name ] ; sh:targetClass biolink:PathologicalAnatomicalExposure . biolink:PathologicalAnatomicalOutcome a sh:NodeShape ; @@ -21089,63 +21089,63 @@ biolink:PathologicalAnatomicalStructure a sh:NodeShape ; sh:description "An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ] ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:PathologicalAnatomicalStructure . biolink:PathologicalEntityMixin a sh:NodeShape ; @@ -21158,7 +21158,20 @@ biolink:PathologicalProcess a sh:NodeShape ; sh:closed true ; sh:description "A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -21168,28 +21181,35 @@ biolink:PathologicalProcess a sh:NodeShape ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 5 ; + sh:path biolink:in_taxon_label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:order 12 ; sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 9 ; sh:path biolink:synonym ], @@ -21198,39 +21218,19 @@ biolink:PathologicalProcess a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_output ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 14 ; sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:in_taxon_label ] ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ] ; sh:targetClass biolink:PathologicalProcess . biolink:PathologicalProcessExposure a sh:NodeShape ; @@ -21238,76 +21238,76 @@ biolink:PathologicalProcessExposure a sh:NodeShape ; sh:description "A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:order 13 ; + sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ] ; + sh:order 5 ; + sh:path biolink:iri ] ; sh:targetClass biolink:PathologicalProcessExposure . biolink:PathologicalProcessOutcome a sh:NodeShape ; @@ -21324,253 +21324,251 @@ biolink:Phenomenon a sh:NodeShape ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path dct:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ] ; sh:targetClass biolink:Phenomenon . biolink:PhenotypicFeatureToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:property [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:double ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:qualifier ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], + sh:order 46 ; + sh:path biolink:object_direction_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:qualifiers ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 41 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:minCount 1 ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 47 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 25 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], + sh:order 43 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:p_value ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 30 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 17 ; + sh:path biolink:original_object ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_evidence ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 48 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:negated ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_percentage ], + sh:order 44 ; + sh:path biolink:subject_direction_qualifier ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 28 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:object_aspect_qualifier ], [ sh:class biolink:Disease ; sh:description "disease" ; sh:maxCount 1 ; @@ -21578,65 +21576,61 @@ biolink:PhenotypicFeatureToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path rdf:object ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], + sh:order 40 ; + sh:path biolink:has_total ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:has_total ], + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:order 39 ; sh:path biolink:has_count ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ] ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ] ; sh:targetClass biolink:PhenotypicFeatureToDiseaseAssociation . biolink:PhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:has_percentage ], + sh:order 5 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:class biolink:PhenotypicFeature ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -21644,140 +21638,108 @@ biolink:PhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path rdf:subject ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:object_direction_qualifier ], + sh:order 10 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:order 3 ; + sh:path biolink:has_quotient ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_aspect_qualifier ], + sh:minCount 1 ; + sh:order 12 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:has_count ], + sh:order 2 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:qualified_predicate ], [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_total ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 1 ; + sh:path biolink:has_count ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path rdf:predicate ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:double ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path rdf:object ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:has_quotient ] ; + sh:order 8 ; + sh:path biolink:object_direction_qualifier ] ; sh:targetClass biolink:PhenotypicFeatureToEntityAssociationMixin . biolink:PhenotypicQuality a sh:NodeShape ; sh:closed true ; sh:description "A property of a phenotype" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 12 ; + sh:path dct:description ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:PhenotypicQuality . - -biolink:PhenotypicSex a sh:NodeShape ; - sh:closed true ; - sh:description "An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 10 ; @@ -21789,38 +21751,73 @@ biolink:PhenotypicSex a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:PhenotypicQuality . + +biolink:PhenotypicSex a sh:NodeShape ; + sh:closed true ; + sh:description "An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:class biolink:NamedThing ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:order 11 ; sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -21830,16 +21827,19 @@ biolink:PhenotypicSex a sh:NodeShape ; sh:maxCount 1 ; sh:order 0 ; sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ] ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ] ; sh:targetClass biolink:PhenotypicSex . biolink:PhysicalEssence a sh:NodeShape ; @@ -21857,226 +21857,241 @@ biolink:PhysicalEssenceOrOccurrent a sh:NodeShape ; biolink:PhysiologicalProcess a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 14 ; sh:path dct:description ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 15 ; + sh:path biolink:has_attribute ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], + sh:order 5 ; + sh:path biolink:in_taxon_label ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 9 ; sh:path biolink:synonym ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], + [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:class biolink:PhysicalEntity ; sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:enabled_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path rdfs:label ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ] ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:id ] ; sh:targetClass biolink:PhysiologicalProcess . biolink:PlanetaryEntity a sh:NodeShape ; sh:closed true ; sh:description "Any entity or process that exists at the level of the whole planet" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:order 7 ; sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 9 ; + sh:path dct:description ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 6 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ] ; + sh:path biolink:category ] ; sh:targetClass biolink:PlanetaryEntity . biolink:Plant a sh:NodeShape ; sh:closed true ; sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; - sh:path biolink:deprecated ] ; + sh:path biolink:deprecated ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:Plant . biolink:Polypeptide a sh:NodeShape ; sh:closed true ; sh:description "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; @@ -22088,38 +22103,66 @@ biolink:Polypeptide a sh:NodeShape ; sh:order 6 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 9 ; + sh:path rdf:type ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 8 ; - sh:path biolink:category ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:path biolink:category ] ; + sh:targetClass biolink:Polypeptide . + +biolink:PopulationToPopulationAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between a two populations" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a human-readable description of an entity" ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "the population that form the subject of the association" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ] ; - sh:targetClass biolink:Polypeptide . - -biolink:PopulationToPopulationAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a two populations" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], @@ -22128,145 +22171,94 @@ biolink:PopulationToPopulationAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that form the subject of the association" ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:description "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "a human-readable description of an entity" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:PopulationOfIndividualOrganisms ; sh:description "the population that form the object of the association" ; sh:maxCount 1 ; @@ -22274,84 +22266,93 @@ biolink:PopulationToPopulationAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "a point in time" ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ] ; - sh:targetClass biolink:PopulationToPopulationAssociation . - -biolink:PosttranslationalModification a sh:NodeShape ; - sh:closed true ; - sh:description "A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ] ; + sh:targetClass biolink:PopulationToPopulationAssociation . + +biolink:PosttranslationalModification a sh:NodeShape ; + sh:closed true ; + sh:description "A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], @@ -22360,127 +22361,133 @@ biolink:PosttranslationalModification a sh:NodeShape ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ] ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ] ; sh:targetClass biolink:PosttranslationalModification . biolink:PreprintPublication a sh:NodeShape ; sh:closed true ; sh:description "a document reresenting an early version of an author's original scholarly work, such as a research paper or a review, prior to formal peer review and publication in a peer-reviewed scholarly or scientific journal." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 19 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:order 17 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:format ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 13 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:id ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:creation_date ], [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:order 18 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:deprecated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ], + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:license ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:rights ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 11 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:license ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:creation_date ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 4 ; + sh:path biolink:mesh_terms ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:summary ], [ sh:datatype xsd:string ; sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; sh:order 6 ; sh:path dct:type ], - [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ] ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:order 3 ; + sh:path biolink:keywords ] ; sh:targetClass biolink:PreprintPublication . biolink:ProcessedMaterial a sh:NodeShape ; sh:closed true ; sh:description "A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:id ], + sh:order 7 ; + sh:path biolink:is_toxic ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 12 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; @@ -22495,67 +22502,46 @@ biolink:ProcessedMaterial a sh:NodeShape ; sh:maxCount 1 ; sh:order 17 ; sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:category ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path dct:description ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 12 ; - sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:iri ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:trade_name ], + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:highest_FDA_approval_status ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ], + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:string ; sh:order 16 ; sh:path rdf:type ], @@ -22563,137 +22549,151 @@ biolink:ProcessedMaterial a sh:NodeShape ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 5 ; sh:path biolink:available_from ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:full_name ] ; + sh:order 14 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:id ] ; sh:targetClass biolink:ProcessedMaterial . biolink:Protein a sh:NodeShape ; sh:closed true ; sh:description "A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ] ; + sh:order 8 ; + sh:path biolink:category ] ; sh:targetClass biolink:Protein . biolink:ProteinDomain a sh:NodeShape ; sh:closed true ; sh:description "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 12 ; sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 6 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 3 ; sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 6 ; - sh:path biolink:synonym ], + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -22709,6 +22709,12 @@ biolink:ProteinFamily a sh:NodeShape ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -22723,136 +22729,159 @@ biolink:ProteinFamily a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_gene_or_gene_product ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 6 ; - sh:path biolink:synonym ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 3 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 11 ; + sh:path rdfs:label ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 9 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 4 ; - sh:path biolink:xref ] ; + sh:path biolink:xref ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 6 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:ProteinFamily . biolink:ProteinIsoform a sh:NodeShape ; sh:closed true ; sh:description "Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ] ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:ProteinIsoform . biolink:RNAProduct a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:property [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; @@ -22862,29 +22891,25 @@ biolink:RNAProduct a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + sh:order 5 ; + sh:path biolink:full_name ] ; + sh:targetClass biolink:RNAProduct . + +biolink:RNAProductIsoform a sh:NodeShape ; + sh:closed true ; + sh:description "Represents a protein that is a specific isoform of the canonical or reference RNA" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -22892,341 +22917,286 @@ biolink:RNAProduct a sh:NodeShape ; sh:order 6 ; sh:path biolink:id ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:RNAProduct . - -biolink:RNAProductIsoform a sh:NodeShape ; - sh:closed true ; - sh:description "Represents a protein that is a specific isoform of the canonical or reference RNA" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 0 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:RNAProductIsoform . - -biolink:ReactionToCatalystAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path rdf:predicate ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:class biolink:MolecularEntity ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:subject ], + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:path biolink:deprecated ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 3 ; + sh:path biolink:in_taxon_label ] ; + sh:targetClass biolink:RNAProductIsoform . + +biolink:ReactionToCatalystAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:iri ], + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 27 ; sh:path biolink:object_namespace ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 35 ; + sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the chemical element that is the target of the statement" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 5 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the chemical element that is the target of the statement" ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:datatype xsd:integer ; + sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:stoichiometry ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 5 ; - sh:path rdf:object ], + sh:order 4 ; + sh:path rdf:predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:integer ; - sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:stoichiometry ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:deprecated ], + [ sh:class biolink:MolecularEntity ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 33 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:description "the side of a reaction being modeled (ie: left or right)" ; - sh:in ( "left" "right" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:reaction_side ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 17 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], + sh:order 37 ; + sh:path rdfs:label ], [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:reaction_direction ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path dct:description ] ; - sh:targetClass biolink:ReactionToCatalystAssociation . - -biolink:ReactionToParticipantAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path dct:description ], - [ sh:class biolink:MolecularEntity ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:subject ], + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:description "the side of a reaction being modeled (ie: left or right)" ; + sh:in ( "left" "right" ) ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], + sh:order 2 ; + sh:path biolink:reaction_side ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:negated ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; + sh:order 34 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path dct:description ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ] ; + sh:targetClass biolink:ReactionToCatalystAssociation . + +biolink:ReactionToParticipantAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 36 ; sh:path rdf:type ], - [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; - sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:reaction_direction ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical element that is the target of the statement" ; + sh:minCount 1 ; + sh:order 33 ; + sh:path biolink:id ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 4 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:description "the side of a reaction being modeled (ie: left or right)" ; + sh:in ( "left" "right" ) ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], + sh:order 2 ; + sh:path biolink:reaction_side ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -23234,135 +23204,111 @@ biolink:ReactionToParticipantAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "a point in time" ; + sh:order 34 ; + sh:path biolink:iri ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 35 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 39 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 35 ; - sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:object_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical element that is the target of the statement" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:description "the side of a reaction being modeled (ie: left or right)" ; - sh:in ( "left" "right" ) ; + sh:order 5 ; + sh:path rdf:object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:reaction_side ], + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 26 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], + sh:order 38 ; + sh:path dct:description ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:p_value ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], + sh:order 10 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:integer ; sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:stoichiometry ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:subject_category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], + sh:order 40 ; + sh:path biolink:deprecated ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -23370,90 +23316,140 @@ biolink:ReactionToParticipantAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 15 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:MolecularEntity ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ] ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; + sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:reaction_direction ] ; sh:targetClass biolink:ReactionToParticipantAssociation . biolink:ReagentTargetedGene a sh:NodeShape ; sh:closed true ; sh:description "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path biolink:id ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:has_biological_sequence ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 11 ; + sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ] ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:ReagentTargetedGene . biolink:RegulatoryRegion a sh:NodeShape ; sh:closed true ; sh:description "A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 11 ; sh:path rdfs:label ], @@ -23461,18 +23457,25 @@ biolink:RegulatoryRegion a sh:NodeShape ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; sh:path biolink:xref ], @@ -23480,37 +23483,34 @@ biolink:RegulatoryRegion a sh:NodeShape ; sh:minCount 1 ; sh:order 9 ; sh:path biolink:category ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:iri ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path rdf:type ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ] ; + sh:order 6 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:RegulatoryRegion . biolink:RelationshipQuantifier a sh:NodeShape ; @@ -23534,42 +23534,39 @@ biolink:RelativeFrequencyAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a relative frequency analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], + sh:order 0 ; + sh:path biolink:license ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 13 ; sh:path dct:description ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 6 ; @@ -23577,10 +23574,9 @@ biolink:RelativeFrequencyAnalysisResult a sh:NodeShape ; [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -23591,76 +23587,110 @@ biolink:RelativeFrequencyAnalysisResult a sh:NodeShape ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ] ; + sh:targetClass biolink:RelativeFrequencyAnalysisResult . + +biolink:SensitivityQuantifier a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:SensitivityQuantifier . + +biolink:SequenceAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between a sequence feature and a nucleic acid entity it is localized to." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:RelativeFrequencyAnalysisResult . - -biolink:SensitivityQuantifier a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:SensitivityQuantifier . - -biolink:SequenceAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a sequence feature and a nucleic acid entity it is localized to." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -23669,15 +23699,20 @@ biolink:SequenceAssociation a sh:NodeShape ; sh:order 12 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -23685,154 +23720,114 @@ biolink:SequenceAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 34 ; + sh:path rdfs:label ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; sh:path biolink:subject_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ] ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ] ; sh:targetClass biolink:SequenceAssociation . biolink:SequenceFeatureRelationship a sh:NodeShape ; sh:closed true ; sh:description "For example, a particular exon is part of a particular transcript or gene" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 32 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -23840,122 +23835,95 @@ biolink:SequenceFeatureRelationship a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:deprecated ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 35 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 31 ; + sh:path biolink:iri ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -23963,84 +23931,94 @@ biolink:SequenceFeatureRelationship a sh:NodeShape ; sh:order 17 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; - sh:path biolink:subject_category_closure ] ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ] ; sh:targetClass biolink:SequenceFeatureRelationship . biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; sh:closed false ; sh:description "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:Treatment ; sh:description "treatment whose efficacy is modulated by the subject variant" ; sh:maxCount 1 ; @@ -24048,199 +24026,181 @@ biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:SequenceVariant ; - sh:description "variant that modulates the treatment of some disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 33 ; sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:SequenceVariant ; + sh:description "variant that modulates the treatment of some disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ] ; - sh:targetClass biolink:SequenceVariantModulatesTreatmentAssociation . - -biolink:Serial a sh:NodeShape ; - sh:closed true ; - sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:creation_date ], + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:volume ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:authors ], - [ sh:datatype xsd:string ; - sh:description "Serials (journals) should have industry-standard identifier such as from ISSN." ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 17 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:full_name ], + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:license ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 16 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ] ; + sh:targetClass biolink:SequenceVariantModulatesTreatmentAssociation . + +biolink:Serial a sh:NodeShape ; + sh:closed true ; + sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 14 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:format ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -24250,52 +24210,92 @@ biolink:Serial a sh:NodeShape ; sh:description "Should generally be set to an ontology class defined term for 'serial' or 'journal'." ; sh:order 20 ; sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 16 ; + sh:path biolink:synonym ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 22 ; - sh:path dct:description ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:order 15 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; - sh:order 21 ; - sh:path rdfs:label ], + sh:order 1 ; + sh:path biolink:volume ], [ sh:datatype xsd:string ; - sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; + sh:description "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:issue ], + sh:order 0 ; + sh:path biolink:iso_abbreviation ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:iri ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:creation_date ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:authors ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path dct:description ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 19 ; sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:deprecated ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; sh:order 9 ; sh:path dct:type ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:rights ], + sh:description "keywords tagging a publication" ; + sh:order 6 ; + sh:path biolink:keywords ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 4 ; - sh:path biolink:pages ], + sh:description "Serials (journals) should have industry-standard identifier such as from ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:iso_abbreviation ], + sh:order 11 ; + sh:path biolink:rights ], [ sh:description "mesh terms tagging a publication" ; sh:order 7 ; sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:format ], + sh:order 10 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:order 6 ; - sh:path biolink:keywords ], + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 4 ; + sh:path biolink:pages ], + [ sh:datatype xsd:string ; + sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:issue ], [ sh:datatype xsd:string ; sh:description "executive summary of a publication" ; sh:maxCount 1 ; @@ -24307,44 +24307,23 @@ biolink:SeverityValue a sh:NodeShape ; sh:closed true ; sh:description "describes the severity of a phenotypic feature or disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 10 ; sh:path biolink:category ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -24354,325 +24333,346 @@ biolink:SeverityValue a sh:NodeShape ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ] ; sh:targetClass biolink:SeverityValue . biolink:SiRNA a sh:NodeShape ; sh:closed true ; sh:description "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ] ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ] ; sh:targetClass biolink:SiRNA . biolink:SmallMolecule a sh:NodeShape ; sh:closed true ; sh:description "A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 2 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:string ; + sh:property [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:has_chemical_role ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:trade_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 4 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:boolean ; sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:is_metabolite ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 2 ; + sh:path biolink:available_from ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:order 13 ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:iri ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:max_tolerated_dose ], + sh:order 17 ; + sh:path biolink:deprecated ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 14 ; sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 10 ; sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:deprecated ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:has_chemical_role ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:order 13 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:is_toxic ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 1 ; + sh:path biolink:trade_name ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:category ] ; + sh:order 3 ; + sh:path biolink:max_tolerated_dose ] ; sh:targetClass biolink:SmallMolecule . biolink:Snv a sh:NodeShape ; sh:closed true ; sh:description "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Gene ; - sh:description "Each allele can be associated with any number of genes" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 5 ; sh:path biolink:provided_by ], - [ sh:description "The state of the sequence w.r.t a reference sequence" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 8 ; sh:path biolink:synonym ], + [ sh:class biolink:Gene ; + sh:description "Each allele can be associated with any number of genes" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 12 ; sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ] ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:in_taxon_label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:description "The state of the sequence w.r.t a reference sequence" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:has_biological_sequence ] ; sh:targetClass biolink:Snv . biolink:SocioeconomicExposure a sh:NodeShape ; sh:closed true ; sh:description "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], + sh:order 13 ; + sh:path dct:description ], [ sh:class biolink:SocioeconomicAttribute ; sh:description "connects any entity to an attribute" ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; sh:path biolink:has_quantitative_value ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:description "a point in time" ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 1 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:order 12 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ] ; + sh:path rdf:type ] ; sh:targetClass biolink:SocioeconomicExposure . biolink:SocioeconomicOutcome a sh:NodeShape ; @@ -24690,162 +24690,138 @@ biolink:Study a sh:NodeShape ; sh:closed true ; sh:description "a detailed investigation and/or analysis" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "Alternate human-readable names for a thing" ; sh:order 3 ; sh:path biolink:synonym ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:order 7 ; - sh:path rdf:type ] ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:Study . biolink:StudyPopulation a sh:NodeShape ; sh:closed true ; sh:description "A group of people banded together or treated as a group as participants in a research study." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ] ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:StudyPopulation . biolink:StudyResult a sh:NodeShape ; sh:closed false ; sh:description "A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 13 ; sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 9 ; @@ -24853,100 +24829,124 @@ biolink:StudyResult a sh:NodeShape ; [ sh:description "Alternate human-readable names for a thing" ; sh:order 7 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:order 11 ; sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ] ; + sh:order 3 ; + sh:path biolink:creation_date ] ; sh:targetClass biolink:StudyResult . biolink:StudyVariable a sh:NodeShape ; sh:closed true ; sh:description "a variable that is used as a measure in the investigation of a study" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path rdf:type ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 12 ; sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:license ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ] ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ] ; sh:targetClass biolink:StudyVariable . biolink:SubjectOfInvestigation a sh:NodeShape ; @@ -24958,77 +24958,34 @@ biolink:SubjectOfInvestigation a sh:NodeShape ; biolink:TaxonToTaxonAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 35 ; sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "An association between individuals of different taxa." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -25036,188 +24993,231 @@ biolink:TaxonToTaxonAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 30 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OrganismTaxon ; - sh:description "An association between individuals of different taxa." ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:object_namespace ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_attribute ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ] ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ] ; sh:targetClass biolink:TaxonToTaxonAssociation . biolink:TextMiningResult a sh:NodeShape ; sh:closed true ; sh:description "A result of text mining." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 13 ; sh:path dct:description ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:rights ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 8 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ] ; sh:targetClass biolink:TextMiningResult . biolink:ThingWithTaxon a sh:NodeShape ; @@ -25239,96 +25239,64 @@ biolink:TranscriptToGeneRelationship a sh:NodeShape ; sh:closed true ; sh:description "A gene is a collection of transcripts" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:property [ sh:class biolink:Gene ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -25336,64 +25304,64 @@ biolink:TranscriptToGeneRelationship a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_subject ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:class biolink:Transcript ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -25401,60 +25369,73 @@ biolink:TranscriptToGeneRelationship a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ] ; - sh:targetClass biolink:TranscriptToGeneRelationship . - -biolink:TranscriptionFactorBindingSite a sh:NodeShape ; - sh:closed true ; - sh:description "A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 12 ; + sh:order 35 ; sh:path dct:description ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; + sh:order 30 ; sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ] ; + sh:targetClass biolink:TranscriptToGeneRelationship . + +biolink:TranscriptionFactorBindingSite a sh:NodeShape ; + sh:closed true ; + sh:description "A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; @@ -25463,218 +25444,359 @@ biolink:TranscriptionFactorBindingSite a sh:NodeShape ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 11 ; sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], + sh:order 1 ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:TranscriptionFactorBindingSite . + +biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 14 ; + sh:order 37 ; sh:path biolink:deprecated ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 39 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:description "The relationship to the disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:TranscriptionFactorBindingSite . - -biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:qualified_predicate ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 42 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:order 40 ; sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:SequenceVariant ; - sh:description "A variant that has a role in modeling the disease." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "The relationship to the disease" ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 43 ; + sh:path biolink:frequency_qualifier ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "a point in time" ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 34 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 35 ; + sh:path dct:description ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:SequenceVariant ; + sh:description "A variant that has a role in modeling the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ] ; + sh:targetClass biolink:VariantAsAModelOfDiseaseAssociation . + +biolink:VariantToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 34 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_attribute ], + [ sh:description "E.g. is pathogenic for" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated in some way with the disease state" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:frequency_qualifier ], + sh:order 38 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -25683,338 +25805,180 @@ biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:order 11 ; sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_direction_qualifier ], + sh:order 40 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ] ; - sh:targetClass biolink:VariantAsAModelOfDiseaseAssociation . - -biolink:VariantToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:class biolink:Disease ; - sh:description "a disease that is associated with that variant" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:frequency_qualifier ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "a point in time" ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 41 ; + sh:path biolink:object_direction_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:subject_direction_qualifier ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 32 ; sh:path biolink:category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "E.g. is pathogenic for" ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:order 35 ; + sh:path dct:description ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_direction_qualifier ], + sh:order 39 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:Disease ; + sh:description "a disease that is associated with that variant" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 30 ; sh:path biolink:id ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated in some way with the disease state" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ] ; + sh:order 43 ; + sh:path biolink:frequency_qualifier ] ; sh:targetClass biolink:VariantToDiseaseAssociation . biolink:VariantToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:property [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated with some other entity" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated with some other entity" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:VariantToEntityAssociationMixin . biolink:VariantToGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:Gene ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -26023,15 +25987,10 @@ biolink:VariantToGeneAssociation a sh:NodeShape ; sh:order 2 ; sh:path rdf:object ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -26039,124 +25998,165 @@ biolink:VariantToGeneAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated with some other entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:object_namespace ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated with some other entity" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ] ; + sh:order 18 ; + sh:path biolink:object_category ] ; sh:targetClass biolink:VariantToGeneAssociation . biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; @@ -26164,273 +26164,240 @@ biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; sh:description "An association between a variant and expression of a gene (i.e. e-QTL)" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 20 ; + sh:path biolink:original_object ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 5 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 6 ; + sh:path rdf:object ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], + sh:order 38 ; + sh:path rdfs:label ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 24 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Optional quantitative value indicating degree of expression." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:quantifier_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 34 ; - sh:path biolink:id ], + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:qualifier ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated with some other entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:iri ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 5 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 39 ; sh:path dct:description ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 36 ; - sh:path biolink:category ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "a point in time" ; + sh:minCount 1 ; + sh:order 34 ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:timepoint ], + sh:order 35 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 37 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], + sh:order 3 ; + sh:path biolink:phenotypic_state ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:deprecated ], [ sh:class biolink:LifeStage ; sh:description "stage during which gene or protein expression of takes place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:stage_qualifier ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 37 ; + sh:path rdf:type ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:phenotypic_state ], + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 36 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 7 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Optional quantitative value indicating degree of expression." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 0 ; + sh:path biolink:quantifier_qualifier ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:original_object ], + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:expression_site ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:subject_label_closure ] ; - sh:targetClass biolink:VariantToGeneExpressionAssociation . - -biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 18 ; + sh:path biolink:original_subject ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated with some other entity" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 4 ; + sh:path rdf:subject ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:has_total ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 11 ; + sh:path biolink:has_evidence ] ; + sh:targetClass biolink:VariantToGeneExpressionAssociation . + +biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_percentage ], + sh:order 41 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:SequenceVariant ; sh:description "a sequence variant in which the allele state is associated in some way with the phenotype state" ; sh:maxCount 1 ; @@ -26442,109 +26409,147 @@ biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 34 ; sh:path rdf:type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:order 47 ; sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 31 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 21 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 44 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:order 43 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], + sh:order 48 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 33 ; + sh:path biolink:category ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -26553,251 +26558,272 @@ biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 12 ; sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:subject_closure ], - [ sh:description "a point in time" ; + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 45 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 36 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ] ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:has_count ] ; sh:targetClass biolink:VariantToPhenotypicFeatureAssociation . biolink:VariantToPopulationAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a variant and a population, where the variant has particular frequency in the population" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 35 ; - sh:path biolink:id ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:agent_type ], - [ sh:class biolink:SequenceVariant ; - sh:description "an allele that has a certain frequency in a given population" ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 38 ; - sh:path rdf:type ], + sh:order 22 ; + sh:path biolink:subject_category ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 31 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:qualifiers ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:iri ], + sh:order 33 ; + sh:path biolink:p_value ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 15 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 12 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 41 ; + sh:path biolink:has_attribute ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:integer ; + sh:description "number all populations that carry a particular allele, aka allele number" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:has_total ], [ sh:datatype xsd:double ; sh:description "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:has_quotient ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_source ], + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:integer ; + sh:description "number in object population that carry a particular allele, aka allele count" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:has_count ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:object_category_closure ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 37 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 15 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 18 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:deprecated ], + sh:order 39 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 35 ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:double ; sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_subject ], + sh:order 13 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "the population that is observed to have the frequency" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:object_namespace ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], + sh:order 10 ; + sh:path biolink:qualifiers ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 21 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 19 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 39 ; - sh:path rdfs:label ], + sh:order 9 ; + sh:path biolink:qualifier ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 40 ; sh:path dct:description ], - [ sh:datatype xsd:integer ; - sh:description "number all populations that carry a particular allele, aka allele number" ; + [ sh:class biolink:SequenceVariant ; + sh:description "an allele that has a certain frequency in a given population" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:has_total ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -26805,93 +26831,69 @@ biolink:VariantToPopulationAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 16 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that is observed to have the frequency" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:integer ; - sh:description "number in object population that carry a particular allele, aka allele count" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:has_count ], + sh:order 42 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:original_object ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 37 ; - sh:path biolink:category ] ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 38 ; + sh:path rdf:type ] ; sh:targetClass biolink:VariantToPopulationAssociation . biolink:Vertebrate a sh:NodeShape ; sh:closed true ; sh:description "A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 8 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 11 ; + sh:path dct:description ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; @@ -26899,132 +26901,118 @@ biolink:Vertebrate a sh:NodeShape ; [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ] ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ] ; sh:targetClass biolink:Vertebrate . biolink:Virus a sh:NodeShape ; sh:closed true ; sh:description "A virus is a microorganism that replicates itself as a microRNA and infects the host cell." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; - sh:path biolink:deprecated ] ; + sh:path biolink:deprecated ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:Virus . biolink:WebPage a sh:NodeShape ; sh:closed true ; sh:description "a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, and/or other features." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:property [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:order 18 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:order 6 ; - sh:path dct:type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 13 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 11 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:license ], + sh:order 15 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:order 17 ; sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:category ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; sh:description "executive summary of a publication" ; sh:maxCount 1 ; @@ -27035,378 +27023,392 @@ biolink:WebPage a sh:NodeShape ; sh:order 19 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:format ], + sh:order 6 ; + sh:path dct:type ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:category ], + sh:order 21 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:rights ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:rights ] ; + sh:order 7 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:id ] ; sh:targetClass biolink:WebPage . biolink:Behavior a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; sh:path biolink:id ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path dct:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:deprecated ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], + sh:order 5 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:iri ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ] ; + [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ] ; sh:targetClass biolink:Behavior . biolink:BehavioralFeature a sh:NodeShape ; sh:closed true ; sh:description "A phenotypic feature which is behavioral in nature." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ] ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ] ; sh:targetClass biolink:BehavioralFeature . biolink:BiologicalProcess a sh:NodeShape ; sh:closed true ; sh:description "One or more causally connected executions of molecular functions" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], + sh:order 15 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:deprecated ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path dct:description ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:in_taxon_label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ] ; sh:targetClass biolink:BiologicalProcess . biolink:CellularComponent a sh:NodeShape ; sh:closed true ; sh:description "A location in or around a cell" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 9 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ] ; + sh:order 7 ; + sh:path biolink:iri ] ; sh:targetClass biolink:CellularComponent . biolink:ClinicalAttribute a sh:NodeShape ; sh:closed true ; sh:description "Attributes relating to a clinical manifestation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 12 ; sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], - [ sh:class biolink:QuantityValue ; + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -27417,429 +27419,427 @@ biolink:ClinicalAttribute a sh:NodeShape ; [ sh:datatype xsd:string ; sh:order 11 ; sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ] ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:ClinicalAttribute . biolink:Dataset a sh:NodeShape ; sh:closed true ; sh:description "an item that refers to a collection of data from a data source." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], + sh:property [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 8 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 13 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:rights ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 7 ; sh:path biolink:synonym ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 12 ; sh:path rdfs:label ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ] ; + sh:order 0 ; + sh:path biolink:license ] ; sh:targetClass biolink:Dataset . biolink:DatasetDistribution a sh:NodeShape ; sh:closed true ; sh:description "an item that holds distribution level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:rights ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:creation_date ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], + sh:order 0 ; + sh:path biolink:distribution_download_url ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 8 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:order 12 ; sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 9 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:format ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:category ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:distribution_download_url ], + sh:order 2 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 5 ; sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:full_name ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:creation_date ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:license ] ; + sh:order 14 ; + sh:path dct:description ] ; sh:targetClass biolink:DatasetDistribution . biolink:Device a sh:NodeShape ; sh:closed true ; sh:description "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 2 ; + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 9 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ] ; - sh:targetClass biolink:Device . - -biolink:Exon a sh:NodeShape ; - sh:closed true ; - sh:description "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; + sh:order 0 ; sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 13 ; + sh:order 11 ; sh:path biolink:deprecated ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "a long-form human readable name for a thing" ; + sh:order 8 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:Device . + +biolink:Exon a sh:NodeShape ; + sh:closed true ; + sh:description "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:in_taxon_label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Exon . biolink:GeneFamily a sh:NodeShape ; sh:closed true ; sh:description "any grouping of multiple genes or gene products related by common descent" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], + sh:order 8 ; + sh:path biolink:iri ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 11 ; sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 12 ; + sh:path dct:description ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], [ sh:class biolink:Gene ; sh:description "connects an entity with one or more gene or gene products" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_gene_or_gene_product ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 6 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 7 ; sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 5 ; - sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 6 ; - sh:path biolink:synonym ] ; + sh:path biolink:full_name ] ; sh:targetClass biolink:GeneFamily . biolink:GeneProductMixin a sh:NodeShape ; sh:closed false ; sh:description "The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA molecules." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:GeneProductMixin . - -biolink:GeneticInheritance a sh:NodeShape ; - sh:closed true ; - sh:description "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:property [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 1 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:GeneProductMixin . + +biolink:GeneticInheritance a sh:NodeShape ; + sh:closed true ; + sh:description "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ] ; + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:GeneticInheritance . biolink:InformationContentEntity a sh:NodeShape ; @@ -27851,63 +27851,63 @@ biolink:InformationContentEntity a sh:NodeShape ; sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], + sh:order 1 ; + sh:path biolink:rights ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:order 11 ; sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:id ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 10 ; @@ -27918,95 +27918,83 @@ biolink:Onset a sh:NodeShape ; sh:closed true ; sh:description "The age group in which (disease) symptom manifestations appear." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 10 ; sh:path biolink:category ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 12 ; sh:path dct:description ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ] ; + sh:path biolink:has_attribute_type ] ; sh:targetClass biolink:Onset . biolink:OrganismalEntity a sh:NodeShape ; sh:closed false ; sh:description "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; @@ -28015,40 +28003,52 @@ biolink:OrganismalEntity a sh:NodeShape ; sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 10 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ] ; + sh:path dct:description ] ; sh:targetClass biolink:OrganismalEntity . biolink:PredicateMapping a sh:NodeShape ; @@ -28056,156 +28056,142 @@ biolink:PredicateMapping a sh:NodeShape ; sh:description "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:mapped_predicate ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:object_part_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:species_context_qualifier ], + sh:order 19 ; + sh:path biolink:narrow_match ], [ sh:datatype xsd:string ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:anatomical_context_qualifier ], + sh:order 14 ; + sh:path biolink:object_context_qualifier ], [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:causal_mechanism_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "holds between two entities that have strictly equivalent meanings, with a high degree of confidence" ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:exact_match ], [ sh:datatype xsd:string ; sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:object_derivative_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:object_form_or_variant_qualifier ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 7 ; sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:object_aspect_qualifier ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:subject_direction_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:object_form_or_variant_qualifier ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:subject_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:subject_part_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:broad_match ], + sh:order 17 ; + sh:path biolink:species_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 3 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:subject_derivative_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], [ sh:class biolink:NamedThing ; - sh:description "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree." ; + sh:description "holds between two entities that have strictly equivalent meanings, with a high degree of confidence" ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:narrow_match ], + sh:order 18 ; + sh:path biolink:exact_match ], [ sh:datatype xsd:string ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:object_context_qualifier ], + sh:order 16 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:broad_match ], [ sh:datatype xsd:string ; - sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:object_part_qualifier ], + sh:order 8 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_form_or_variant_qualifier ] ; + sh:order 0 ; + sh:path biolink:mapped_predicate ], + [ sh:datatype xsd:string ; + sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:subject_part_qualifier ] ; sh:targetClass biolink:PredicateMapping . biolink:Procedure a sh:NodeShape ; sh:closed true ; sh:description "A series of actions conducted in a certain order or manner" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -28213,39 +28199,35 @@ biolink:Procedure a sh:NodeShape ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:order 7 ; - sh:path rdf:type ] ; - sh:targetClass biolink:Procedure . - -biolink:SocioeconomicAttribute a sh:NodeShape ; - sh:closed true ; - sh:description "Attributes relating to a socioeconomic manifestation" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:order 11 ; sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 5 ; + sh:order 4 ; sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ] ; + sh:targetClass biolink:Procedure . + +biolink:SocioeconomicAttribute a sh:NodeShape ; + sh:closed true ; + sh:description "Attributes relating to a socioeconomic manifestation" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -28253,40 +28235,58 @@ biolink:SocioeconomicAttribute a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ] ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:SocioeconomicAttribute . biolink:TaxonomicRank a sh:NodeShape ; @@ -28305,16 +28305,54 @@ biolink:Treatment a sh:NodeShape ; sh:closed true ; sh:description "A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:property [ sh:class biolink:Procedure ; + sh:description "connects an entity to one or more (medical) procedures" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_procedure ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], + [ sh:class biolink:Drug ; + sh:description "connects an entity to one or more drugs" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_drug ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:timepoint ], + [ sh:description "Alternate human-readable names for a thing" ; sh:order 7 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 10 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -28325,89 +28363,46 @@ biolink:Treatment a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_device ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:class biolink:Drug ; - sh:description "connects an entity to one or more drugs" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_drug ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 8 ; sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Procedure ; - sh:description "connects an entity to one or more (medical) procedures" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_procedure ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:Treatment . biolink:Zygosity a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], + sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:order 12 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 10 ; @@ -28416,9 +28411,6 @@ biolink:Zygosity a sh:NodeShape ; sh:maxCount 1 ; sh:order 0 ; sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -28426,10 +28418,6 @@ biolink:Zygosity a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -28440,202 +28428,214 @@ biolink:Zygosity a sh:NodeShape ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ] ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:Zygosity . biolink:Case a sh:NodeShape ; sh:closed true ; sh:description "An individual (human) organism that has a patient role in some clinical context." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:property [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; - sh:path biolink:deprecated ] ; + sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:Case . biolink:CellLine a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ] ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:CellLine . biolink:IndividualOrganism a sh:NodeShape ; sh:closed true ; sh:description "An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:order 11 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ] ; + sh:order 9 ; + sh:path rdf:type ] ; sh:targetClass biolink:IndividualOrganism . biolink:Outcome a sh:NodeShape ; @@ -28648,50 +28648,34 @@ biolink:Transcript a sh:NodeShape ; sh:closed true ; sh:description "An RNA synthesized on a DNA or RNA template by an RNA polymerase." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -28700,12 +28684,28 @@ biolink:Transcript a sh:NodeShape ; [ sh:description "Alternate human-readable names for a thing" ; sh:order 5 ; sh:path biolink:synonym ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; - sh:path biolink:xref ] ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ] ; sh:targetClass biolink:Transcript . biolink:Drug a sh:NodeShape ; @@ -28716,110 +28716,110 @@ biolink:Drug a sh:NodeShape ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 10 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:max_tolerated_dose ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 15 ; sh:path biolink:category ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_chemical_role ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 6 ; + sh:path biolink:available_from ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:deprecated ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 17 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:is_toxic ], + sh:order 1 ; + sh:path biolink:is_supplement ], [ sh:datatype xsd:string ; - sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:drug_regulatory_status_world_wide ], + sh:order 2 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:trade_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 11 ; - sh:path biolink:xref ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 4 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:max_tolerated_dose ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 4 ; + sh:path biolink:routes_of_delivery ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:order 16 ; - sh:path rdf:type ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 6 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:string ; - sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:boolean ; + sh:description "" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:iri ], + sh:order 8 ; + sh:path biolink:is_toxic ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 11 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:is_supplement ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + sh:order 5 ; + sh:path biolink:trade_name ], + [ sh:datatype xsd:string ; + sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ] ; + sh:order 3 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_chemical_role ] ; sh:targetClass biolink:Drug . biolink:ExposureEvent a sh:NodeShape ; sh:closed false ; sh:description "A (possibly time bounded) incidence of a feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; - sh:path biolink:id ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ] ; + sh:path biolink:id ] ; sh:targetClass biolink:ExposureEvent . biolink:MaterialSample a sh:NodeShape ; @@ -28829,6 +28829,15 @@ biolink:MaterialSample a sh:NodeShape ; sh:property [ sh:datatype xsd:string ; sh:order 7 ; sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; @@ -28836,6 +28845,14 @@ biolink:MaterialSample a sh:NodeShape ; [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:full_name ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 9 ; @@ -28843,38 +28860,21 @@ biolink:MaterialSample a sh:NodeShape ; [ sh:description "Alternate human-readable names for a thing" ; sh:order 3 ; sh:path biolink:synonym ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:id ] ; sh:targetClass biolink:MaterialSample . biolink:Pathway a sh:NodeShape ; @@ -28883,32 +28883,47 @@ biolink:Pathway a sh:NodeShape ; sh:property [ sh:datatype xsd:string ; sh:order 12 ; sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path dct:description ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ], [ sh:class biolink:PhysicalEntity ; sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:enabled_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], + sh:order 0 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 5 ; @@ -28916,53 +28931,45 @@ biolink:Pathway a sh:NodeShape ; [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ] ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:Pathway . biolink:LifeStage a sh:NodeShape ; sh:closed true ; sh:description "A stage of development or growth of an organism, including post-natal adult stages" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 8 ; @@ -28971,41 +28978,27 @@ biolink:LifeStage a sh:NodeShape ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], @@ -29013,155 +29006,156 @@ biolink:LifeStage a sh:NodeShape ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ] ; + sh:order 1 ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:LifeStage . biolink:NucleicAcidEntity a sh:NodeShape ; sh:closed true ; sh:description "A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:has_attribute ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 6 ; - sh:path biolink:available_from ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:trade_name ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 10 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 11 ; - sh:path biolink:xref ], + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], + sh:order 15 ; + sh:path biolink:category ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 13 ; sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:is_toxic ], + sh:order 4 ; + sh:path biolink:is_metabolite ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "indicates whether a molecular entity is a metabolite" ; + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:is_metabolite ], + sh:order 7 ; + sh:path biolink:max_tolerated_dose ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 17 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:order 16 ; sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 10 ; + sh:path biolink:provided_by ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 6 ; + sh:path biolink:available_from ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 11 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:boolean ; + sh:description "" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:is_toxic ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; - sh:path biolink:has_biological_sequence ] ; + sh:path biolink:has_biological_sequence ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:NucleicAcidEntity . biolink:MolecularActivity a sh:NodeShape ; sh:closed true ; sh:description "An execution of a molecular function carried out by a gene product or macromolecular complex." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:in_taxon_label ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:class biolink:MolecularEntity ; + sh:description "A chemical entity that is the input for the reaction" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path dct:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -29172,91 +29166,97 @@ biolink:MolecularActivity a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; sh:path biolink:enabled_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:MolecularEntity ; - sh:description "A chemical entity that is the output for the reaction" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:id ], [ sh:class biolink:MolecularEntity ; - sh:description "A chemical entity that is the input for the reaction" ; + sh:description "A chemical entity that is the output for the reaction" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ] ; + sh:order 2 ; + sh:path biolink:has_output ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:MolecularActivity . biolink:PopulationOfIndividualOrganisms a sh:NodeShape ; sh:closed true ; sh:description "A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ] ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ] ; sh:targetClass biolink:PopulationOfIndividualOrganisms . biolink:MacromolecularMachineMixin a sh:NodeShape ; @@ -29273,93 +29273,95 @@ biolink:MolecularEntity a sh:NodeShape ; sh:closed true ; sh:description "A molecular entity is a chemical entity composed of individual or covalently bonded atoms." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path rdfs:label ], + sh:order 15 ; + sh:path dct:description ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:category ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "indicates whether a molecular entity is a metabolite" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:is_metabolite ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:deprecated ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 2 ; - sh:path biolink:available_from ], + [ sh:datatype xsd:string ; + sh:order 13 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:max_tolerated_dose ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:trade_name ], - [ sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:order 13 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:order 0 ; + sh:path biolink:is_metabolite ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:is_toxic ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 17 ; + sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:has_chemical_role ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path rdfs:label ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 2 ; + sh:path biolink:available_from ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ] ; + sh:description "" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:trade_name ] ; sh:targetClass biolink:MolecularEntity . biolink:PhysicalEntity a sh:NodeShape ; sh:closed true ; sh:description "An entity that has material reality (a.k.a. physical essence)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 6 ; @@ -29374,34 +29376,32 @@ biolink:PhysicalEntity a sh:NodeShape ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 3 ; sh:path biolink:synonym ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path dct:description ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 8 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; @@ -29418,404 +29418,403 @@ biolink:Genotype a sh:NodeShape ; sh:closed true ; sh:description "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Zygosity ; + sh:property [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_zygosity ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 4 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 5 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 7 ; + sh:path biolink:full_name ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:in_taxon ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:in_taxon_label ], + sh:order 9 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:full_name ], + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:class biolink:Zygosity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_zygosity ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 13 ; sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ] ; + sh:order 14 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Genotype . -biolink:PhenotypicFeature a sh:NodeShape ; - sh:closed true ; - sh:description "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; +biolink:PhenotypicFeature a sh:NodeShape ; + sh:closed true ; + sh:description "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:PhenotypicFeature . - -biolink:SequenceVariant a sh:NodeShape ; - sh:closed true ; - sh:description "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; + sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 13 ; + sh:order 11 ; sh:path dct:description ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ] ; + sh:targetClass biolink:PhenotypicFeature . + +biolink:SequenceVariant a sh:NodeShape ; + sh:closed true ; + sh:description "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], - [ sh:class biolink:Gene ; - sh:description "Each allele can be associated with any number of genes" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 6 ; sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 10 ; sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:Gene ; + sh:description "Each allele can be associated with any number of genes" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 9 ; + sh:path biolink:iri ], [ sh:description "The state of the sequence w.r.t a reference sequence" ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 4 ; + sh:path biolink:in_taxon_label ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], + sh:order 13 ; + sh:path dct:description ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 7 ; - sh:path biolink:full_name ] ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:SequenceVariant . biolink:ChemicalEntity a sh:NodeShape ; sh:closed true ; sh:description "A chemical entity is a physical entity that pertains to chemistry or biochemistry." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:is_toxic ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 8 ; - sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:id ], + sh:order 0 ; + sh:path biolink:trade_name ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 14 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:deprecated ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:max_tolerated_dose ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_chemical_role ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:trade_name ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:is_toxic ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:id ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ] ; + [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ] ; sh:targetClass biolink:ChemicalEntity . biolink:Agent a sh:NodeShape ; sh:closed true ; sh:description "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." ; + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:address ], - [ sh:description "a human-readable description of an entity" ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations." ; - sh:order 0 ; - sh:path biolink:affiliation ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations." ; + sh:order 0 ; + sh:path biolink:affiliation ], + [ sh:datatype xsd:string ; + sh:description "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 1 ; + sh:path biolink:address ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ] ; + sh:order 4 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:Agent . biolink:ChemicalRole a sh:NodeShape ; sh:closed true ; sh:description "A role played by the molecular entity or part thereof within a chemical context." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], + sh:order 4 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:order 11 ; sh:path rdf:type ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 0 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -29823,37 +29822,31 @@ biolink:ChemicalRole a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 14 ; - sh:path biolink:deprecated ] ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ] ; sh:targetClass biolink:ChemicalRole . biolink:DiseaseOrPhenotypicFeature a sh:NodeShape ; sh:closed true ; sh:description "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; @@ -29862,60 +29855,71 @@ biolink:DiseaseOrPhenotypicFeature a sh:NodeShape ; sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:in_taxon ] ; + sh:path biolink:in_taxon ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeature . biolink:Gene a sh:NodeShape ; sh:closed true ; sh:description "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Symbol for a particular thing" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:symbol ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -29925,73 +29929,78 @@ biolink:Gene a sh:NodeShape ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:has_biological_sequence ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Symbol for a particular thing" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:symbol ], + sh:order 11 ; + sh:path rdf:type ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 8 ; + sh:path biolink:synonym ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 13 ; sh:path dct:description ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 8 ; - sh:path biolink:synonym ] ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ] ; sh:targetClass biolink:Gene . biolink:BiologicalSex a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 10 ; sh:path biolink:category ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -29999,99 +30008,59 @@ biolink:BiologicalSex a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ] ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:BiologicalSex . biolink:Disease a sh:NodeShape ; sh:closed true ; sh:description "A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 8 ; @@ -30099,17 +30068,48 @@ biolink:Disease a sh:NodeShape ; [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:in_taxon_label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ] ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Disease . biolink:AnatomicalEntity a sh:NodeShape ; @@ -30117,63 +30117,63 @@ biolink:AnatomicalEntity a sh:NodeShape ; sh:description "A subcellular location, cell type or gross anatomical part" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:in_taxon ] ; + sh:path biolink:in_taxon ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ] ; sh:targetClass biolink:AnatomicalEntity . biolink:GeneOrGeneProduct a sh:NodeShape ; @@ -30205,87 +30205,115 @@ biolink:OrganismTaxon a sh:NodeShape ; sh:closed true ; sh:description "A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:order 8 ; - sh:path rdf:type ], + sh:order 9 ; + sh:path rdfs:label ], + [ sh:class biolink:TaxonomicRank ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_taxonomic_rank ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 1 ; sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 4 ; - sh:path biolink:synonym ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:deprecated ], - [ sh:class biolink:TaxonomicRank ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_taxonomic_rank ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path rdf:type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 4 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 2 ; sh:path biolink:xref ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path dct:description ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:full_name ] ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ] ; sh:targetClass biolink:OrganismTaxon . biolink:EvidenceType a sh:NodeShape ; sh:closed true ; sh:description "Class of evidence that supports an association" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:creation_date ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:id ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 7 ; sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 10 ; @@ -30295,150 +30323,121 @@ biolink:EvidenceType a sh:NodeShape ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + sh:order 9 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ] ; + sh:path biolink:license ] ; sh:targetClass biolink:EvidenceType . biolink:NamedThing a sh:NodeShape ; sh:closed true ; sh:description "a databased entity or concept/class" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ] ; + sh:order 8 ; + sh:path rdfs:label ] ; sh:targetClass biolink:NamedThing . biolink:Publication a sh:NodeShape ; sh:closed true ; sh:description "Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:format ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:deprecated ], + sh:order 8 ; + sh:path biolink:rights ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:rights ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:license ], + sh:description "keywords tagging a publication" ; + sh:order 3 ; + sh:path biolink:keywords ], [ sh:datatype xsd:string ; sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:summary ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:order 6 ; + sh:path dct:type ], [ sh:description "mesh terms tagging a publication" ; sh:order 4 ; sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], + sh:order 17 ; + sh:path rdf:type ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; @@ -30448,164 +30447,187 @@ biolink:Publication a sh:NodeShape ; sh:order 5 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:order 6 ; - sh:path dct:type ], + sh:order 7 ; + sh:path biolink:license ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:deprecated ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 11 ; sh:path biolink:provided_by ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], [ sh:datatype xsd:string ; - sh:order 17 ; - sh:path rdf:type ], + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:format ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:category ] ; + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 1 ; + sh:path biolink:pages ] ; sh:targetClass biolink:Publication . biolink:RetrievalSource a sh:NodeShape ; sh:closed true ; sh:description "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge." ; - sh:in ( "primary_knowledge_source" "aggregator_knowledge_source" "supporting_data_source" ) ; + sh:property [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:resource_role ], + sh:order 7 ; + sh:path biolink:creation_date ], [ sh:description "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; sh:path biolink:resource_id ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:order 14 ; - sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 18 ; sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:description "The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:upstream_resource_ids ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:format ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 8 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], + sh:order 5 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:order 14 ; + sh:path rdf:type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:license ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:id ], + [ sh:description "The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:upstream_resource_ids ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 15 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 8 ; - sh:path biolink:provided_by ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:license ], + [ sh:description "The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge." ; + sh:in ( "primary_knowledge_source" "aggregator_knowledge_source" "supporting_data_source" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:resource_role ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:id ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 16 ; + sh:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:creation_date ] ; + sh:order 9 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:RetrievalSource . biolink:Attribute a sh:NodeShape ; sh:closed true ; sh:description "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 9 ; sh:path biolink:synonym ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; sh:order 11 ; sh:path rdf:type ], @@ -30613,37 +30635,15 @@ biolink:Attribute a sh:NodeShape ; sh:minCount 1 ; sh:order 10 ; sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ] ; + sh:order 0 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Attribute . biolink:OntologyClass a sh:NodeShape ; diff --git a/src/biolink_model/datamodel/model.py b/src/biolink_model/datamodel/model.py index 00842bba2..4c6005099 100644 --- a/src/biolink_model/datamodel/model.py +++ b/src/biolink_model/datamodel/model.py @@ -1,5 +1,5 @@ # Auto generated from biolink_model.yaml by pythongen.py version: 0.0.1 -# Generation date: 2024-07-25T17:45:18 +# Generation date: 2024-07-25T17:51:17 # Schema: Biolink-Model # # id: https://w3id.org/biolink/biolink-model diff --git a/src/biolink_model/schema/biolink_model.yaml b/src/biolink_model/schema/biolink_model.yaml index da453c72a..28a336ba4 100644 --- a/src/biolink_model/schema/biolink_model.yaml +++ b/src/biolink_model/schema/biolink_model.yaml @@ -7054,8 +7054,6 @@ classes: - STY:T075 # Drug Delivery Device - STY:T203 - # Biomedical or Dental Material - - STY:T122 diagnostic aid: is_a: named thing diff --git a/src/biolink_model/scripts/classprefixes.py b/src/biolink_model/scripts/classprefixes.py index e36eaf2b6..aa4b5a4e6 100644 --- a/src/biolink_model/scripts/classprefixes.py +++ b/src/biolink_model/scripts/classprefixes.py @@ -1,5 +1,5 @@ # Auto generated from class_prefixes.yaml by pythongen.py version: 0.0.1 -# Generation date: 2024-07-25T17:46:11 +# Generation date: 2024-07-25T17:52:08 # Schema: BiolinkClassPrefixes # # id: biolink-model-class-prefixes