regenerate artifacts

biolink · Nov 11, 2024 · 8d12025 · 8d12025
2 parents 2e116b8 + f5558c4
commit 8d12025
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Showing 13 changed files with 25,124 additions and 24,641 deletions.
diff --git a/biolink-model.yaml b/biolink-model.yaml
@@ -9872,6 +9872,7 @@ classes:
     mixins:
       - chemical to entity association mixin
       - entity to disease or phenotypic feature association mixin
+      - entity to feature or disease qualifiers mixin
     slots:
       - FDA adverse event level
     slot_usage:
@@ -10355,6 +10356,7 @@ classes:
       - object aspect qualifier
       - object direction qualifier
       - qualified predicate
+      - disease context qualifier
 
   feature or disease qualifiers to entity mixin:
     description: >-
@@ -10383,6 +10385,8 @@ classes:
       - object specialization qualifier
       - anatomical context qualifier
     defining_slots:
+      - subject
+      - predicate
       - object
     slot_usage:
       object:

diff --git a/project/graphql/biolink_model.graphql b/project/graphql/biolink_model.graphql
@@ -833,6 +833,7 @@ type CellLineAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMi
     objectAspectQualifier: String
     objectDirectionQualifier: DirectionQualifierEnum
     qualifiedPredicate: String
+    diseaseContextQualifier: Disease
   }
 
 type CellLineToDiseaseOrPhenotypicFeatureAssociation implements CellLineToEntityAssociationMixin, EntityToDiseaseOrPhenotypicFeatureAssociationMixin
@@ -1243,10 +1244,17 @@ type ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation im
     type: [String]
     category: [Uriorcurie]
     fDAAdverseEventLevel: FDAIDAAdverseEventEnum
+    frequencyQualifier: FrequencyValue
+    subjectAspectQualifier: String
+    subjectDirectionQualifier: DirectionQualifierEnum
+    objectAspectQualifier: String
+    objectDirectionQualifier: DirectionQualifierEnum
+    qualifiedPredicate: String
+    diseaseContextQualifier: Disease
     predicate: PredicateType!
   }
 
-type ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation implements ChemicalToEntityAssociationMixin, EntityToDiseaseOrPhenotypicFeatureAssociationMixin
+type ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation implements ChemicalToEntityAssociationMixin, EntityToDiseaseOrPhenotypicFeatureAssociationMixin, EntityToFeatureOrDiseaseQualifiersMixin
   {
     id: String!
     iri: IriType
@@ -1288,6 +1296,13 @@ type ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation implements
     category: [Uriorcurie]
     fDAAdverseEventLevel: FDAIDAAdverseEventEnum
     predicate: PredicateType!
+    frequencyQualifier: FrequencyValue
+    subjectAspectQualifier: String
+    subjectDirectionQualifier: DirectionQualifierEnum
+    objectAspectQualifier: String
+    objectDirectionQualifier: DirectionQualifierEnum
+    qualifiedPredicate: String
+    diseaseContextQualifier: Disease
   }
 
 type ChemicalRole
@@ -2540,6 +2555,7 @@ interface EntityToDiseaseAssociationMixin
     objectAspectQualifier: String
     objectDirectionQualifier: DirectionQualifierEnum
     qualifiedPredicate: String
+    diseaseContextQualifier: Disease
     object: Disease!
   }
 
@@ -2568,6 +2584,7 @@ interface EntityToFeatureOrDiseaseQualifiersMixin
     objectAspectQualifier: String
     objectDirectionQualifier: DirectionQualifierEnum
     qualifiedPredicate: String
+    diseaseContextQualifier: Disease
   }
 
 interface EntityToOutcomeAssociationMixin
@@ -4073,6 +4090,7 @@ type GenotypeAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMi
     objectAspectQualifier: String
     objectDirectionQualifier: DirectionQualifierEnum
     qualifiedPredicate: String
+    diseaseContextQualifier: Disease
     subject: Genotype!
   }
 
@@ -4123,6 +4141,7 @@ type GenotypeToDiseaseAssociation implements GenotypeToEntityAssociationMixin, E
     objectAspectQualifier: String
     objectDirectionQualifier: DirectionQualifierEnum
     qualifiedPredicate: String
+    diseaseContextQualifier: Disease
   }
 
 interface GenotypeToEntityAssociationMixin
@@ -5670,6 +5689,7 @@ type OrganismalEntityAsAModelOfDiseaseAssociation implements ModelToDiseaseAssoc
     objectAspectQualifier: String
     objectDirectionQualifier: DirectionQualifierEnum
     qualifiedPredicate: String
+    diseaseContextQualifier: Disease
   }
 
 interface Outcome
@@ -5986,6 +6006,7 @@ type PhenotypicFeatureToDiseaseAssociation implements EntityToDiseaseAssociation
     objectAspectQualifier: String
     objectDirectionQualifier: DirectionQualifierEnum
     qualifiedPredicate: String
+    diseaseContextQualifier: Disease
     sexQualifier: BiologicalSex
     hasCount: Integer
     hasTotal: Integer
@@ -7348,6 +7369,7 @@ type VariantAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMix
     objectAspectQualifier: String
     objectDirectionQualifier: DirectionQualifierEnum
     qualifiedPredicate: String
+    diseaseContextQualifier: Disease
     subject: SequenceVariant!
   }
 
@@ -7398,6 +7420,7 @@ type VariantToDiseaseAssociation implements VariantToEntityAssociationMixin, Ent
     objectAspectQualifier: String
     objectDirectionQualifier: DirectionQualifierEnum
     qualifiedPredicate: String
+    diseaseContextQualifier: Disease
   }
 
 interface VariantToEntityAssociationMixin

diff --git 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": "2024-11-07T16:11:25",
+      "generation_date": "2024-11-11T12:07:21",
       "source": "biolink_model.yaml"
    },
    "@context": {

diff --git a/project/jsonld/biolink_model.jsonld b/project/jsonld/biolink_model.jsonld
@@ -4659,6 +4659,7 @@
       "slot_uri": "https://w3id.org/biolink/vocab/disease_context_qualifier",
       "owner": "EntityToPhenotypicFeatureAssociationMixin",
       "domain_of": [
+        "EntityToFeatureOrDiseaseQualifiersMixin",
         "EntityToPhenotypicFeatureAssociationMixin"
       ],
       "range": "Disease",
@@ -31056,7 +31057,8 @@
       "is_a": "Association",
       "mixins": [
         "ChemicalToEntityAssociationMixin",
-        "EntityToDiseaseOrPhenotypicFeatureAssociationMixin"
+        "EntityToDiseaseOrPhenotypicFeatureAssociationMixin",
+        "EntityToFeatureOrDiseaseQualifiersMixin"
       ],
       "slots": [
         "id",
@@ -31098,7 +31100,14 @@
         "association_type",
         "association_category",
         "FDA_adverse_event_level",
-        "chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association_predicate"
+        "chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association_predicate",
+        "frequency_qualifier",
+        "subject_aspect_qualifier",
+        "subject_direction_qualifier",
+        "object_aspect_qualifier",
+        "object_direction_qualifier",
+        "qualified_predicate",
+        "disease_context_qualifier"
       ],
       "slot_usage": {},
       "class_uri": "https://w3id.org/biolink/vocab/ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation",
@@ -31159,6 +31168,13 @@
         "association_type",
         "association_category",
         "FDA_adverse_event_level",
+        "frequency_qualifier",
+        "subject_aspect_qualifier",
+        "subject_direction_qualifier",
+        "object_aspect_qualifier",
+        "object_direction_qualifier",
+        "qualified_predicate",
+        "disease_context_qualifier",
         "chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association_predicate"
       ],
       "slot_usage": {},
@@ -32119,7 +32135,8 @@
         "subject_direction_qualifier",
         "object_aspect_qualifier",
         "object_direction_qualifier",
-        "qualified_predicate"
+        "qualified_predicate",
+        "disease_context_qualifier"
       ],
       "slot_usage": {},
       "class_uri": "https://w3id.org/biolink/vocab/EntityToFeatureOrDiseaseQualifiersMixin",
@@ -32179,6 +32196,8 @@
       "slot_usage": {},
       "class_uri": "https://w3id.org/biolink/vocab/EntityToPhenotypicFeatureAssociationMixin",
       "defining_slots": [
+        "subject",
+        "predicate",
         "object"
       ],
       "@type": "ClassDefinition"
@@ -32364,6 +32383,7 @@
         "object_aspect_qualifier",
         "object_direction_qualifier",
         "qualified_predicate",
+        "disease_context_qualifier",
         "entity_to_disease_association_mixin_object"
       ],
       "slot_usage": {},
@@ -33458,6 +33478,7 @@
         "object_aspect_qualifier",
         "object_direction_qualifier",
         "qualified_predicate",
+        "disease_context_qualifier",
         "sex_qualifier",
         "has_count",
         "has_total",
@@ -33845,7 +33866,8 @@
         "subject_direction_qualifier",
         "object_aspect_qualifier",
         "object_direction_qualifier",
-        "qualified_predicate"
+        "qualified_predicate",
+        "disease_context_qualifier"
       ],
       "slot_usage": {},
       "class_uri": "https://w3id.org/biolink/vocab/VariantToDiseaseAssociation",
@@ -33912,7 +33934,8 @@
         "subject_direction_qualifier",
         "object_aspect_qualifier",
         "object_direction_qualifier",
-        "qualified_predicate"
+        "qualified_predicate",
+        "disease_context_qualifier"
       ],
       "slot_usage": {},
       "class_uri": "https://w3id.org/biolink/vocab/GenotypeToDiseaseAssociation",
@@ -34065,6 +34088,7 @@
         "object_aspect_qualifier",
         "object_direction_qualifier",
         "qualified_predicate",
+        "disease_context_qualifier",
         "variant_as_a_model_of_disease_association_subject"
       ],
       "slot_usage": {},
@@ -34130,6 +34154,7 @@
         "object_aspect_qualifier",
         "object_direction_qualifier",
         "qualified_predicate",
+        "disease_context_qualifier",
         "genotype_as_a_model_of_disease_association_subject"
       ],
       "slot_usage": {},
@@ -34195,7 +34220,8 @@
         "subject_direction_qualifier",
         "object_aspect_qualifier",
         "object_direction_qualifier",
-        "qualified_predicate"
+        "qualified_predicate",
+        "disease_context_qualifier"
       ],
       "slot_usage": {},
       "class_uri": "https://w3id.org/biolink/vocab/CellLineAsAModelOfDiseaseAssociation",
@@ -34260,7 +34286,8 @@
         "subject_direction_qualifier",
         "object_aspect_qualifier",
         "object_direction_qualifier",
-        "qualified_predicate"
+        "qualified_predicate",
+        "disease_context_qualifier"
       ],
       "slot_usage": {},
       "class_uri": "https://w3id.org/biolink/vocab/OrganismalEntityAsAModelOfDiseaseAssociation",
@@ -35871,9 +35898,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "biolink_model.yaml",
-  "source_file_date": "2024-11-07T16:11:20",
-  "source_file_size": 403672,
-  "generation_date": "2024-11-07T16:11:27",
+  "source_file_date": "2024-11-11T12:07:16",
+  "source_file_size": 403774,
+  "generation_date": "2024-11-11T12:07:24",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/biolink_model.context.jsonld",