Merge pull request #1534 from biolink/extension_qualifier

add subject/object specialization qualifier to help represent extensions in MAXO and GO-CAM
biolink · Nov 11, 2024 · 4b37138 · 4b37138
2 parents f5558c4 + 8d12025
commit 4b37138
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Showing 13 changed files with 25,803 additions and 24,623 deletions.
diff --git a/biolink-model.yaml b/biolink-model.yaml
@@ -1316,6 +1316,26 @@ slots:
     in_subset:
       - translator_minimal
 
+  specialization qualifier:
+    is_a: qualifier
+    abstract: true
+    description: >-
+      A qualifier that composes with a core subject/object concept to define a more specific version of the 
+      subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept 
+      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"
+
   aspect qualifier:
     is_a: qualifier
     abstract: true
@@ -1440,6 +1460,17 @@ slots:
     in_subset:
       - translator_minimal
 
+  subject specialization qualifier:
+    is_a: specialization qualifier
+    description: >-
+      A qualifier that composes with a core subject/object concept to define a more specific version of the 
+      subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept 
+      and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the
+      subject identifier.
+    in_subset:
+      - translator_minimal
+    range: uriorcurie
+
   subject form or variant qualifier:
     description: >-
       A qualifier that composes with a core subject/object concept to define a specific type, variant,
@@ -1506,6 +1537,17 @@ slots:
     in_subset:
       - translator_minimal
 
+  object specialization qualifier:
+    is_a: specialization qualifier
+    description: >-
+      A qualifier that composes with a core subject/object concept to define a more specific version of the 
+      subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept 
+      and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the
+      subject identifier.
+    in_subset:
+      - translator_minimal
+    range: uriorcurie
+
   object form or variant qualifier:
     description: >-
       A qualifier that composes with a core subject/object concept to define a specific type, variant,
@@ -9821,7 +9863,7 @@ classes:
   chemical or drug or treatment to disease or phenotypic feature association:
     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.
+      where the disease or phenotypic feature is a secondary undesirable effect.
     is_a: association
     defining_slots:
       - subject
@@ -10338,7 +10380,13 @@ classes:
       - predicate
       - object
       - sex qualifier
+      - disease context qualifier
+      - subject specialization qualifier
+      - 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
@@ -402,8 +402,11 @@ type BehaviorToBehavioralFeatureAssociation implements EntityToPhenotypicFeature
     objectAspectQualifier: String
     objectDirectionQualifier: DirectionQualifierEnum
     qualifiedPredicate: String
-    diseaseContextQualifier: Disease
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -678,8 +681,11 @@ type CaseToPhenotypicFeatureAssociation implements EntityToPhenotypicFeatureAsso
     objectAspectQualifier: String
     objectDirectionQualifier: DirectionQualifierEnum
     qualifiedPredicate: String
-    diseaseContextQualifier: Disease
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -731,8 +737,11 @@ type CausalGeneToDiseaseAssociation implements EntityToDiseaseAssociationMixin,
     subjectDirectionQualifier: DirectionQualifierEnum
     objectAspectQualifier: String
     qualifiedPredicate: String
-    diseaseContextQualifier: Disease
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -1886,8 +1895,11 @@ type CorrelatedGeneToDiseaseAssociation implements EntityToDiseaseAssociationMix
     subjectDirectionQualifier: DirectionQualifierEnum
     objectAspectQualifier: String
     qualifiedPredicate: String
-    diseaseContextQualifier: Disease
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -2269,8 +2281,11 @@ type DiseaseToPhenotypicFeatureAssociation implements FrequencyQuantifier, Entit
     objectAspectQualifier: String
     objectDirectionQualifier: DirectionQualifierEnum
     qualifiedPredicate: String
-    diseaseContextQualifier: Disease
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
   }
 
 type Drug implements ChemicalOrDrugOrTreatment, OntologyClass
@@ -2458,8 +2473,11 @@ type DruggableGeneToDiseaseAssociation implements EntityToDiseaseAssociationMixi
     subjectDirectionQualifier: DirectionQualifierEnum
     objectAspectQualifier: String
     qualifiedPredicate: String
-    diseaseContextQualifier: Disease
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -2629,11 +2647,14 @@ type EntityToPhenotypicFeatureAssociationMixin implements FrequencyQuantifier
     objectAspectQualifier: String
     objectDirectionQualifier: DirectionQualifierEnum
     qualifiedPredicate: String
-    diseaseContextQualifier: Disease
     subject: NamedThing!
     predicate: PredicateType!
     object: PhenotypicFeature!
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -2917,8 +2938,11 @@ type ExposureEventToPhenotypicFeatureAssociation implements EntityToPhenotypicFe
     objectAspectQualifier: String
     objectDirectionQualifier: DirectionQualifierEnum
     qualifiedPredicate: String
-    diseaseContextQualifier: Disease
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -3185,8 +3209,11 @@ type GeneAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMixin,
     subjectDirectionQualifier: DirectionQualifierEnum
     objectAspectQualifier: String
     qualifiedPredicate: String
-    diseaseContextQualifier: Disease
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -3271,8 +3298,11 @@ type GeneHasVariantThatContributesToDiseaseAssociation
     subjectDirectionQualifier: DirectionQualifierEnum
     objectAspectQualifier: String
     qualifiedPredicate: String
-    diseaseContextQualifier: Disease
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -3394,8 +3424,11 @@ type GeneToDiseaseAssociation implements EntityToDiseaseAssociationMixin, GeneTo
     subjectDirectionQualifier: DirectionQualifierEnum
     objectAspectQualifier: String
     qualifiedPredicate: String
-    diseaseContextQualifier: Disease
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -3451,8 +3484,11 @@ type GeneToDiseaseOrPhenotypicFeatureAssociation implements EntityToPhenotypicFe
     subjectDirectionQualifier: DirectionQualifierEnum
     objectAspectQualifier: String
     qualifiedPredicate: String
-    diseaseContextQualifier: Disease
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -3861,8 +3897,11 @@ type GeneToPhenotypicFeatureAssociation implements EntityToPhenotypicFeatureAsso
     subjectDirectionQualifier: DirectionQualifierEnum
     objectAspectQualifier: String
     qualifiedPredicate: String
-    diseaseContextQualifier: Disease
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -4245,8 +4284,11 @@ type GenotypeToPhenotypicFeatureAssociation implements EntityToPhenotypicFeature
     objectAspectQualifier: String
     objectDirectionQualifier: DirectionQualifierEnum
     qualifiedPredicate: String
-    diseaseContextQualifier: Disease
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -6043,6 +6085,9 @@ type PhenotypicFeatureToPhenotypicFeatureAssociation implements PhenotypicFeatur
     hasQuotient: Double
     hasPercentage: Double
     diseaseContextQualifier: Disease
+    subjectSpecializationQualifier: Uriorcurie
+    objectSpecializationQualifier: Uriorcurie
+    anatomicalContextQualifier: String
   }
 
 type PhenotypicQuality
@@ -7522,8 +7567,11 @@ type VariantToPhenotypicFeatureAssociation implements VariantToEntityAssociation
     objectAspectQualifier: String
     objectDirectionQualifier: DirectionQualifierEnum
     qualifiedPredicate: String
-    diseaseContextQualifier: Disease
     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": "2024-11-11T18:36:13",
+      "generation_date": "2024-11-11T12:07:21",
       "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"
@@ -2166,6 +2170,9 @@
       "source_web_page": {
          "@id": "source_web_page"
       },
+      "specialization_qualifier": {
+         "@id": "specialization_qualifier"
+      },
       "species_context_qualifier": {
          "@type": "@id",
          "@id": "species_context_qualifier"
@@ -2257,6 +2264,10 @@
       "subject_part_qualifier": {
          "@id": "subject_part_qualifier"
       },
+      "subject_specialization_qualifier": {
+         "@type": "xsd:anyURI",
+         "@id": "subject_specialization_qualifier"
+      },
       "summary": {
          "@id": "summary"
       },