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add subject/object specialization qualifier to help represent extensions in MAXO and GO-CAM #1534

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Nov 11, 2024
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add subject/object specialization qualifier to help represent extensions in MAXO and GO-CAM #1534

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2b9d726
add subject and object specialization qualfiiers to handle MAXO and p…
sierra-moxon Nov 8, 2024
2e116b8
adjust format
sierra-moxon Nov 8, 2024
8d12025
regenerate artifacts
sierra-moxon Nov 11, 2024
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50 changes: 49 additions & 1 deletion biolink-model.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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:
Expand Down
78 changes: 63 additions & 15 deletions project/graphql/biolink_model.graphql
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -6043,6 +6085,9 @@ type PhenotypicFeatureToPhenotypicFeatureAssociation implements PhenotypicFeatur
hasQuotient: Double
hasPercentage: Double
diseaseContextQualifier: Disease
subjectSpecializationQualifier: Uriorcurie
objectSpecializationQualifier: Uriorcurie
anatomicalContextQualifier: String
}

type PhenotypicQuality
Expand Down Expand Up @@ -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
Expand Down
13 changes: 12 additions & 1 deletion project/jsonld/biolink_model.context.jsonld
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Original file line number Diff line number Diff line change
@@ -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": {
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -2257,6 +2264,10 @@
"subject_part_qualifier": {
"@id": "subject_part_qualifier"
},
"subject_specialization_qualifier": {
"@type": "xsd:anyURI",
"@id": "subject_specialization_qualifier"
},
"summary": {
"@id": "summary"
},
Expand Down
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