diff --git a/schema/var-pathogenicity-source.yaml b/schema/var-pathogenicity-source.yaml index 18619cc8..963ea9dd 100644 --- a/schema/var-pathogenicity-source.yaml +++ b/schema/var-pathogenicity-source.yaml @@ -4,45 +4,18 @@ type: object strict: true imports: - gks.common: gks.common-source.yaml - vrs: vrs-source.yaml - catvrs: catvrs-source.yaml - annot: annotation-source.yaml + va.core: core-im-source.yaml + gks.common: imports/gks.common-source.yaml + catvrs: imports/catvrs-source.yaml + vrs: imports/vrs-source.yaml namespaces: - gks.common: gks.common.json#/$defs/ - catvrs: catvrs.json#/$defs/ - vrs: vrs.json#/$defs/ - annot: annotation.json#/$defs/ + va.core: core-im.json#/$defs/ + gks.common: imports/gks.common.json#/$defs/ + catvrs: imports/catvrs.json#/$defs/ + vrs: imports/vrs.json#/$defs/ $defs: - VariantStatement: - inherits: annot:Statement - description: >- - A :ref:`Statement` describing the impact of a variant. - heritableProperties: - variant: - extends: subject - oneOf: - - $refCurie: vrs:Variation - - $refCurie: catvrs:CategoricalVariation - - $refCurie: gks.common:IRI - description: A variant that is the subject of the Statement. - - VariantClassification: - inherits: VariantStatement - description: >- - A :ref:`VariantStatement` classifying the impact of a variant. - heritableProperties: - classification: - oneOf: - - $refCurie: gks.common:Coding - - $refCurie: gks.common:IRI - description: >- - A methodological, summary classification about the impact of a variant. - heritableRequired: - - classification - VariantPathogenicity: type: object maturity: Alpha @@ -94,131 +67,4 @@ $defs: A gene context that qualifies the Statement. $refCurie: gks.common:Gene required: - - condition - - VariantStudySummary: - inherits: VariantStatement - description: >- - A :ref:`Statement` summarizing evidence about the impact of a variant from - one or more studies. - heritableProperties: - isReportedIn: - extends: isReportedIn - minItems: 1 - heritableRequired: - - isReportedIn - - VariantOncogenicityStudy: - type: object - inherits: VariantStudySummary - maturity: Alpha - description: >- - A study summarization supporting or refuting the effect of variant on oncogenesis of a tumor type. - properties: - type: - type: string - const: "VariantOncogenicity" - default: "VariantOncogenicity" - description: >- - MUST be "VariantOncogenicity". - predicate: - extends: predicate - enum: - - isOncogenicFor - - isProtectiveFor - - isPredisposingFor - tumorType: - extends: object - oneOf: - - $refCurie: gks.common:Condition - - $refCurie: gks.common:IRI - description: >- - The tumor type for which the variant impact is evaluated. - qualifiers: - extends: qualifiers - properties: - alleleOrigin: - type: string - description: >- - Whether the statement should be interpreted in the context of an inherited - (germline) variant, an acquired (somatic) mutation, or both (combined). - enum: - - germline - - somatic - - combined - allelePrevalence: - type: string - description: >- - Whether the statement should be interpreted in the context of the variant - being rare or common. - enum: - - rare - - common - geneContext: - description: >- - A gene context that qualifies the Statement. - $refCurie: gks.common:Gene - required: - - tumorType - - predicate - - VariantTherapeuticResponseStudy: - type: object - maturity: Alpha - inherits: VariantStudySummary - description: >- - A study summarization describing the role of a variant in modulating the response of a - neoplasm to drug administration or other therapeutic procedure. - properties: - type: - type: string - const: "VariantTherapeuticResponseStudy" - default: "VariantTherapeuticResponseStudy" - description: >- - MUST be "VariantTherapeuticResponseStudy". - predicate: - extends: predicate - enum: - - predictsSensitivityTo - - predictsResistanceTo - therapeutic: - description: A drug administration or other therapeutic procedure that the neoplasm - is intended to respond to. - extends: object - oneOf: - - $refCurie: gks.common:TherapeuticProcedure - - $refCurie: gks.common:IRI - tumorType: - oneOf: - - $refCurie: gks.common:Condition - - $refCurie: gks.common:IRI - description: >- - The tumor type context in which the variant impact is evaluated. - qualifiers: - extends: qualifiers - properties: - alleleOrigin: - type: string - description: >- - Whether the statement should be interpreted in the context of an inherited - (germline) variant, an acquired (somatic) mutation, or both (combined). - enum: - - germline - - somatic - - combined - allelePrevalence: - type: string - description: >- - Whether the statement should be interpreted in the context of the variant - being rare or common. - enum: - - rare - - common - geneContext: - description: >- - A gene context that qualifies the Statement. - $refCurie: gks.common:Gene - required: - - tumorType - - predicate - - therapeutic \ No newline at end of file + - condition \ No newline at end of file