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biolink · Nov 8, 2024 · 2e116b8 · 2e116b8
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Showing 13 changed files with 25,450 additions and 24,422 deletions.
diff --git a/biolink-model.yaml b/biolink-model.yaml
@@ -1325,16 +1325,16 @@ slots:
       and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the
       subject identifier.
     examples:
-        - value: CHEBI:5118  # fluoxetine
-          description: >-
-            In a MAXO annotation this would be a specialization in treatment of a disease. For example, 
-            fluoxetine would be a specialization of the MAXO term 'serotonin-norepinephrine reuptake inhibitor agent 
-            therapy' as a treatment for the HP term 'Fatigable muscle weakness' in the context of the MONDO term
-            'congenital myasthenic syndrome '4A.'
-        - value: GO:0005634  # nucleus
-          description: >-
-            In an expression annotation this would be a specialization in location of an anatomical entity. For example,
-            "expression in the nucleus of hepatic cells" would be a specialization of "expression in hepatic cells"
+      - value: CHEBI:5118  # fluoxetine
+        description: >-
+          In a MAXO annotation this would be a specialization in treatment of a disease. For example, 
+          fluoxetine would be a specialization of the MAXO term 'serotonin-norepinephrine reuptake inhibitor agent 
+          therapy' as a treatment for the HP term 'Fatigable muscle weakness' in the context of the MONDO term
+          'congenital myasthenic syndrome '4A.'
+      - value: GO:0005634  # nucleus
+        description: >-
+          In an expression annotation this would be a specialization in location of an anatomical entity. For example,
+          "expression in the nucleus of hepatic cells" would be a specialization of "expression in hepatic cells"
 
   aspect qualifier:
     is_a: qualifier

diff --git a/project/graphql/biolink_model.graphql b/project/graphql/biolink_model.graphql
@@ -404,6 +404,9 @@ type BehaviorToBehavioralFeatureAssociation implements EntityToPhenotypicFeature
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
     diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -680,6 +683,9 @@ type CaseToPhenotypicFeatureAssociation implements EntityToPhenotypicFeatureAsso
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
     diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -733,6 +739,9 @@ type CausalGeneToDiseaseAssociation implements EntityToDiseaseAssociationMixin,
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
     diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -1873,6 +1882,9 @@ type CorrelatedGeneToDiseaseAssociation implements EntityToDiseaseAssociationMix
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
     diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -2256,6 +2268,9 @@ type DiseaseToPhenotypicFeatureAssociation implements FrequencyQuantifier, Entit
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
     diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
   }
 
 type Drug implements ChemicalOrDrugOrTreatment, OntologyClass
@@ -2445,6 +2460,9 @@ type DruggableGeneToDiseaseAssociation implements EntityToDiseaseAssociationMixi
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
     diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -2617,6 +2635,9 @@ type EntityToPhenotypicFeatureAssociationMixin implements FrequencyQuantifier
     object: PhenotypicFeature!
     sexQualifier: BiologicalSex
     diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -2902,6 +2923,9 @@ type ExposureEventToPhenotypicFeatureAssociation implements EntityToPhenotypicFe
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
     diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -3170,6 +3194,9 @@ type GeneAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMixin,
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
     diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -3256,6 +3283,9 @@ type GeneHasVariantThatContributesToDiseaseAssociation
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
     diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -3379,6 +3409,9 @@ type GeneToDiseaseAssociation implements EntityToDiseaseAssociationMixin, GeneTo
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
     diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -3436,6 +3469,9 @@ type GeneToDiseaseOrPhenotypicFeatureAssociation implements EntityToPhenotypicFe
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
     diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -3846,6 +3882,9 @@ type GeneToPhenotypicFeatureAssociation implements EntityToPhenotypicFeatureAsso
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
     diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -4228,6 +4267,9 @@ type GenotypeToPhenotypicFeatureAssociation implements EntityToPhenotypicFeature
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
     diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -6022,6 +6064,9 @@ type PhenotypicFeatureToPhenotypicFeatureAssociation implements PhenotypicFeatur
     hasQuotient: Double
     hasPercentage: Double
     diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
   }
 
 type PhenotypicQuality
@@ -7501,6 +7546,9 @@ type VariantToPhenotypicFeatureAssociation implements VariantToEntityAssociation
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
     diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double

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": "2024-11-07T15:54:30",
+      "generation_date": "2024-11-07T16:11:25",
       "source": "biolink_model.yaml"
    },
    "@context": {
@@ -1845,6 +1845,10 @@
       "object_part_qualifier": {
          "@id": "object_part_qualifier"
       },
+      "object_specialization_qualifier": {
+         "@type": "xsd:anyURI",
+         "@id": "object_specialization_qualifier"
+      },
       "occurs_in": {
          "@type": "@id",
          "@id": "occurs_in"
@@ -2261,6 +2265,7 @@
          "@id": "subject_part_qualifier"
       },
       "subject_specialization_qualifier": {
+         "@type": "xsd:anyURI",
          "@id": "subject_specialization_qualifier"
       },
       "summary": {