split pathogenicity

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
+      - condition