example implementation of is_a

schema/va-spec/core-im/core-im-source.yaml

@@ -13,6 +13,16 @@ namespaces:
   catvrs: ../../catvrs/catvrs.json#/$defs/
   vrs: ../../vrs/vrs.json#/$defs/
 
+$slotdefs:
+  subject:
+    description: The subject slot of a class using the SPOQ terms.
+  predicate:
+    description: The predicate slot of a class using the SPOQ terms.
+  object:
+    description: The object slot of a class using the SPOQ terms.
+  qualifier:
+    description: A qualifier slot of a class using the SPOQ terms.
+
 $defs:
   InformationEntity:
     inherits: gks.common:Entity
@@ -302,35 +312,10 @@ $defs:
     inherits: InformationEntity
     description: >-
       A Statement (aka "Assertion") represents a claim of purported truth as made by a particular agent,
-      on a particular occasion.
+      on a particular occasion. In addition to the properties shared by all Statements, statements MUST
+      also have properties inheriting from Subject<ref> and Predicate<ref>, MAY also have a property inheriting
+      from Object<ref> and MAY also have one or more properties inheriting from Qualifier<ref>.
     heritableProperties:
-      subject:
-        oneOf: 
-          - type: string
-        description: The subject of the Statement.
-      predicate:
-        type: string
-        description: The predicate of the Statement.
-      object:
-        oneOf: 
-          - type: string
-        description: The object of the Statement.
-#  Note that the `qualifier` property below is a *placeholder* that should not be inherited or used 
-#  as is in dervied Statement profiles. It is meant to be specialized into more specifc properties
-#  that are defined to capture a specifc kind of qualifying information relevant to a particular 
-#  Statement profile. e.g. for a VariantPathogenicityStatement, it is specalized into 
-#  'modeOfInheritanceQualifier' and 'geneContextQualifier' properties. 
-#  Commenting out this property for now to aviod its unwanted inheritance in Statement profiles.
-#  Ww will re-instate this property once we determine if/how the metaschema processer can evolve to support
-#  the use case described in the 'comment' below, and discussed in va-spec issue #134.
-#
-#     qualifier:
-#       type: object
-#       placeholder: true      # example of what a flag on core-im properties meant to be placeholders might look like
-#       description: >-
-#         An additional piece of information that extends or refines the meaning of the core 
-#         subject-predicate-object 'triple' - by providing additional details, precision, or 
-#         constraining the statement to apply in a particular context.
       direction:
         type: string
         enum:
@@ -397,7 +382,6 @@ $defs:
           a Statement directly to a piece of evidence supporting it, bypassing the Evidence Line class
           when used data creators do not utilize an Evidence Line object.
     heritableRequired:
-      - subject
       - direction
 
   StudyResult:

schema/va-spec/profiles/json/VariantPathogenicityStatement

@@ -154,7 +154,10 @@
          "default": "VariantPathogenicityStatement",
          "description": "MUST be \"VariantPathogenicityStatement\"."
       },
-      "subjectVariant": {
+      "variant": {
+         "is_a": {
+            "$ref": "../core-im/core-im.json#/$slotdefs/subject"
+         },
          "oneOf": [
             {
                "$ref": "/ga4gh/schema/catvrs/1.x/json/CategoricalVariation"
@@ -168,12 +171,16 @@
          ],
          "description": "A variant that is the subject of the Statement."
       },
-      "predicate": {
-         "type": "string",
-         "description": "The predicate of the Statement.",
+      "causality": {
+         "is_a": {
+            "$ref": "../core-im/core-im.json#/$slotdefs/predicate"
+         },
          "const": "isCausalFor"
       },
-      "objectCondition": {
+      "condition": {
+         "is_a": {
+            "$ref": "../core-im/core-im.json#/$slotdefs/object"
+         },
          "oneOf": [
             {
                "$ref": "/ga4gh/schema/gks-common/1.x/json/IRI"
@@ -184,7 +191,10 @@
          ],
          "description": "The Condition for which the variant impact is stated."
       },
-      "penetranceQualifier": {
+      "penetrance": {
+         "is_a": {
+            "$ref": "../core-im/core-im.json#/$slotdefs/qualifier"
+         },
          "type": "string",
          "enum": [
             "high",
@@ -193,7 +203,10 @@
          ],
          "description": "Extends the statement to report the penetrance of the pathogenic effect - i.e. the extent  to which the variant impact is expressed by individuals carrying it as a measure of the  proportion of carriers exhibiting the condition."
       },
-      "modeOfInheritanceQualifier": {
+      "modeOfInheritance": {
+         "is_a": {
+            "$ref": "../core-im/core-im.json#/$slotdefs/qualifier"
+         },
          "type": "string",
          "enum": [
             "autosomal dominant",
@@ -204,18 +217,21 @@
          ],
          "description": "Reports a pattern of inheritance expected for the pathogenic effect of the variant. "
       },
-      "geneContextQualifier": {
+      "geneContext": {
+         "is_a": {
+            "$ref": "../core-im/core-im.json#/$slotdefs/qualifier"
+         },
          "description": "Reports the gene through which the pathogenic effect asserted for the variant is mediated  (i.e. it is the variant's impact on this gene that is responsible for causing the condition).",
          "$ref": "/ga4gh/schema/gks-domain-entities/1.x/json/Gene"
       }
    },
    "required": [
+      "causality",
+      "condition",
       "direction",
       "id",
-      "objectCondition",
-      "predicate",
-      "subjectVariant",
-      "type"
+      "type",
+      "variant"
    ],
    "additionalProperties": false
 }

schema/va-spec/profiles/profiles-source.yaml

@@ -12,6 +12,7 @@ imports:
 
 namespaces:
   va.core: ../core-im/core-im.json#/$defs/
+  va.core.slots: ../core-im/core-im.json#/$slotdefs/
   gks.common: ../../gks-common/common.json#/$defs/
   gks.domain-entities: ../../gks-domain-entities/domain-entities.json#/$defs/
   catvrs: ../../catvrs/catvrs.json#/$defs/
@@ -153,19 +154,19 @@ $defs:
         default: "VariantDiagnosticStudyStatement"
         description: MUST be "VariantDiagnosticStudyStatement".
       subjectVariant:
-        extends: subject
+        # extends: subject
         oneOf:
         - $refCurie: vrs:Variation
         - $refCurie: catvrs:CategoricalVariation
         - $refCurie: gks.common:IRI
         description: A variant that is the subject of the Statement.
       predicate:
-        extends: predicate
+        # extends: predicate
         enum:
         - positive
         - negative
       objectDisease:
-        extends: object
+        # extends: object
         oneOf:
         - $refCurie: gks.domain-entities:Condition
         - $refCurie: gks.common:IRI
@@ -216,20 +217,20 @@ $defs:
         default: "VariantOncogenicityStatement"
         description: MUST be "VariantOncogenicityStatement".
       subjectVariant:
-        extends: subject
+        # extends: subject
         oneOf:
         - $refCurie: vrs:Variation
         - $refCurie: catvrs:CategoricalVariation
         - $refCurie: gks.common:IRI
         description: A variant that is the subject of the Statement.
       predicate:
-        extends: predicate
+        # extends: predicate
         enum:
         - isOncogenicFor
         - isProtectiveFor
         - isPredisposingFor
       objectTumorType:
-        extends: object
+        # extends: object
         oneOf:
         - $refCurie: gks.domain-entities:Condition
         - $refCurie: gks.common:IRI
@@ -279,23 +280,28 @@ $defs:
         const: "VariantPathogenicityStatement"
         default: "VariantPathogenicityStatement"
         description: MUST be "VariantPathogenicityStatement".
-      subjectVariant:
-        extends: subject
+      variant:
+        is_a:
+          $refCurie: va.core.slots:subject
         oneOf:
         - $refCurie: vrs:Variation
         - $refCurie: catvrs:CategoricalVariation
         - $refCurie: gks.common:IRI
         description: A variant that is the subject of the Statement.
-      predicate:
-        extends: predicate
+      causality:
+        is_a:
+          $refCurie: va.core.slots:predicate
         const: isCausalFor
-      objectCondition:
-        extends: object
+      condition:
+        is_a:
+          $refCurie: va.core.slots:object
         oneOf:
         - $refCurie: gks.domain-entities:Condition
         - $refCurie: gks.common:IRI
         description: The :ref:`Condition` for which the variant impact is stated.    
-      penetranceQualifier:
+      penetrance:
+        is_a:
+          $refCurie: va.core.slots:qualifier
         type: string
         enum:
         - high
@@ -305,7 +311,9 @@ $defs:
           Extends the statement to report the penetrance of the pathogenic effect - i.e. the extent 
           to which the variant impact is expressed by individuals carrying it as a measure of the 
           proportion of carriers exhibiting the condition.
-      modeOfInheritanceQualifier:
+      modeOfInheritance:
+        is_a:
+          $refCurie: va.core.slots:qualifier
         type: string
         enum:
         - autosomal dominant
@@ -315,15 +323,17 @@ $defs:
         - mitochondrial
         description: >-
           Reports a pattern of inheritance expected for the pathogenic effect of the variant. 
-      geneContextQualifier:
+      geneContext:
+        is_a:
+          $refCurie: va.core.slots:qualifier
         description: >-
           Reports the gene through which the pathogenic effect asserted for the variant is mediated 
           (i.e. it is the variant's impact on this gene that is responsible for causing the condition).
         $refCurie: gks.domain-entities:Gene
     required:
-    - subjectVariant
-    - predicate
-    - objectCondition
+    - variant
+    - causality
+    - condition
 
 # Variant Prognostic Study Statement
   VariantPrognosticStudyStatement:
@@ -340,19 +350,19 @@ $defs:
         default: "VariantPrognosticStudyStatement"
         description: MUST be "VariantPrognosticStudyStatement".
       subjectVariant:
-        extends: subject
+        # extends: subject
         oneOf:
         - $refCurie: vrs:Variation
         - $refCurie: catvrs:CategoricalVariation
         - $refCurie: gks.common:IRI
         description: A variant that is the subject of the Statement.
       predicate:
-        extends: predicate
+        # extends: predicate
         enum:
         - Better Outcome
         - Worse Outcome
       objectDisease:
-        extends: object
+        # extends: object
         oneOf:
         - $refCurie: gks.domain-entities:Condition
         - $refCurie: gks.common:IRI
@@ -401,21 +411,21 @@ $defs:
         default: "VariantTherapeuticResponseStudyStatement"
         description: MUST be "VariantTherapeuticResponseStudyStatement".
       subjectVariant:
-        extends: subject
+        # extends: subject
         oneOf:
         - $refCurie: vrs:Variation
         - $refCurie: catvrs:CategoricalVariation
         - $refCurie: gks.common:IRI
         description: A variant that is the subject of the Statement.
       predicate:
-        extends: predicate
+        # extends: predicate
         enum:
         - predictsSensitivityTo
         - predictsResistanceTo
       objectTherapeutic:
         description: A drug administration or other therapeutic procedure that the neoplasm
           is intended to respond to.
-        extends: object
+        # extends: object
         oneOf:
         - $refCurie: gks.domain-entities:TherapeuticProcedure
         - $refCurie: gks.common:IRI