reset baseline copyConstraint from discussions at ashg unconference

ga4gh · Nov 5, 2024 · b112bb6 · b112bb6
1 parent e9c7ce6
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diff --git a/examples/canonicalAllele-ex1.yaml b/examples/canonicalAllele-ex1.yaml
@@ -2,7 +2,7 @@ id: clinvar:662001
 label: NM_004958.4(MTOR):c.5992_5993del (p.Met1998fs)
 type: CategoricalVariant
 constraints:
-  - type: DefiningAlleleContext
+  - type: DefiningAlleleConstraint
     allele:
       id: ga4gh:VA.PN-6_l2_yI1UPBRCtFnWkR52iZXKVJ8b
       type: Allele

diff --git a/examples/categoricalCnv-ex1.yaml b/examples/categoricalCnv-ex1.yaml
@@ -2,9 +2,9 @@ id: clinvar:151061
 type: CategoricalVariant
 label: GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3
 constraints:
-  - type: CopyCountConstraint
+  - type: CopyConstraint
     copies: 3
-  - type: DefiningLocationContext
+  - type: DefiningLocationConstraint
     location:
       type: SequenceLocation
       start: [null, 5945462]

diff --git a/examples/categoricalCnv-ex2.yaml b/examples/categoricalCnv-ex2.yaml
@@ -2,12 +2,9 @@ id: clinvar:151061
 type: CategoricalVariant
 label: GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3
 constraints:
-  - type: CopyChangeConstraint
-    copyChange:
-      system: https://www.ebi.ac.uk/ols4/search?ontology=efo&q=
-      code: EFO:0030070
-      label: Copy Number Gain
-  - type: DefiningLocationContext
+  - type: CopyConstraint
+    copyChange: EFO:0030070
+  - type: DefiningLocationConstraint
     location:
       type: SequenceLocation
       start: [null, 5945462]

diff --git a/examples/proteinSequenceConsequence-ex1.yaml b/examples/proteinSequenceConsequence-ex1.yaml
@@ -11,7 +11,7 @@ description: >-
   treating patients that failed to respond to earlier generation TKI therapies.
 label: EGFR L858R
 constraints:
-  - type: "DefiningAlleleContext"
+  - type: DefiningAlleleConstraint
     allele: vrs.json#/ga4gh:VA.kgjrhgf84CEndyLjKdAO0RxN-e3pJjxA
 members:
   - vrs.json#/ga4gh:VA.7jX7fHgVEqx4C4jMRyZOH0ZBHnLn7_gJ

diff --git a/schema/cat-vrs/cat-vrs-source.yaml b/schema/cat-vrs/cat-vrs-source.yaml
@@ -17,10 +17,10 @@ $defs:
   CategoricalVariant:
     type: object
     inherits: gks-core:Entity
-    maturity: draft
+    maturity: trial use
     description: >-
       A representation of a categorically-defined domain for variation, in which individual
-      contextual variation instances may be members of the domain.
+      Constraintual variation instances may be members of the domain.
     properties:
       type:
         extends: type
@@ -31,7 +31,7 @@ $defs:
         type: array
         ordered: false
         description: >-
-          A non-exhaustive list of VRS variation contexts that satisfy the constraints of
+          A non-exhaustive list of VRS variation Constraints that satisfy the constraints of
           this categorical variant.
         items:
           oneOf:
@@ -56,22 +56,21 @@ $defs:
   # =============================================================================
 
   Constraint:
-    maturity: draft
+    maturity: trial use
     description: >-
       Constraints are used to construct an intensional semantics of categorical variant types.
     oneOf:
-      - $ref: "#/$defs/DefiningAlleleContext"
-      - $ref: "#/$defs/DefiningLocationContext"
-      - $ref: "#/$defs/CopyCountConstraint"
-      - $ref: "#/$defs/CopyChangeConstraint"
+      - $ref: "#/$defs/DefiningAlleleConstraint"
+      - $ref: "#/$defs/DefiningLocationConstraint"
+      - $ref: "#/$defs/CopyConstraint"
     heritableProperties:
       type:
         type: string
     heritableRequired:
       - type
 
-  DefiningAlleleContext:
-    maturity: draft
+  DefiningAlleleConstraint:
+    maturity: trial use
     type: object
     inherits: Constraint
     description: >-
@@ -80,9 +79,9 @@ $defs:
     properties:
       type:
         extends: type
-        const: DefiningAlleleContext
-        default: DefiningAlleleContext
-        description: 'MUST be "DefiningAlleleContext"'
+        const: DefiningAlleleConstraint
+        default: DefiningAlleleConstraint
+        description: 'MUST be "DefiningAlleleConstraint"'
       allele:
         oneOf:
           - $ref: /ga4gh/schema/vrs/2.x/json/Allele
@@ -100,16 +99,16 @@ $defs:
             - translates_to
             - translates_through
         description: >-
-          Defined relationships from which members relate to the defining context.
+          Defined relationships from which members relate to the defining allele.
           ``sequence_liftover`` refers to variants or locations that represent a congruent concept on a differing assembly of a
           human genome (e.g. "GRCh37" and "GRCh38") or gene (e.g. Locus Reference Genomic) sequence. ``transcript_projection``
           refers to variants or locations that occur on transcripts projected from the defined genomic concept. ``codon_translation``
           refers to variants or locations that translate from the codon(s) represented by the defined concept.
     required:
       - allele
 
-  DefiningLocationContext:
-    maturity: draft
+  DefiningLocationConstraint:
+    maturity: trial use
     type: object
     inherits: Constraint
     description: >-
@@ -118,9 +117,9 @@ $defs:
     properties:
       type:
         extends: type
-        const: DefiningLocationContext
-        default: DefiningLocationContext
-        description: 'MUST be "DefiningLocationContext"'
+        const: DefiningLocationConstraint
+        default: DefiningLocationConstraint
+        description: 'MUST be "DefiningLocationConstraint"'
       location:
         oneOf:
           - $ref: /ga4gh/schema/vrs/2.x/json/SequenceLocation
@@ -138,7 +137,7 @@ $defs:
             - translates_to
             - translates_through
         description: >-
-          Defined relationships from which members relate to the defining context.
+          Defined relationships from which members relate to the defining location.
           ``sequence_liftover`` refers to variants or locations that represent a congruent concept on a differing assembly of a
           human genome (e.g. "GRCh37" and "GRCh38") or gene (e.g. Locus Reference Genomic) sequence. ``transcript_projection``
           refers to variants or locations that occur on transcripts projected from the defined genomic concept. ``codon_translation``
@@ -156,50 +155,37 @@ $defs:
       - location
       - matchCharacteristic
 
-  CopyCountConstraint:
-    maturity: draft
+  CopyConstraint:
+    maturity: trial use
     inherits: Constraint
     type: object
     description:
-      The absolute number of copies in a system
+      The quantity of copies or the type of copy change that a member of this
+      categorical variant must have. One and only one MUST be specified.
     properties:
       type:
         extends: type
-        const: CopyCountConstraint
-        default: CopyCountConstraint
-        description: 'MUST be "CopyCountConstraint"'
+        const: CopyConstraint
+        default: CopyConstraint
+        description: 'MUST be "CopyConstraint"'
       copies:
+        description: >-
+          The precise value or range of copies a member of this categorical
+          variant must have.
         oneOf:
-          - type: integer
-          - $ref: /ga4gh/schema/vrs/2.x/json/Range
-    required:
-      - copies
-
-  CopyChangeConstraint:
-    maturity: draft
-    inherits: Constraint
-    type: object
-    description:
-      A representation of copy number change
-    properties:
-      type:
-        extends: type
-        const: CopyChangeConstraint
-        default: CopyChangeConstraint
-        description: 'MUST be "CopyChangeConstraint"'
+        - type: integer
+        - $ref: /ga4gh/schema/vrs/2.x/json/Range
       copyChange:
-        $ref: /ga4gh/schema/gks-core/1.x/json/Coding
-        items:
-          properties:
-            code:
-              enum:
-                - EFO:0030069
-                - EFO:0020073
-                - EFO:0030068
-                - EFO:0030067
-                - EFO:0030064
-                - EFO:0030070
-                - EFO:0030071
-                - EFO:0030072
-    required:
-      - copyChange
+        description: >-
+          The type of copy change a member of this categorical variant must
+          have.
+        type: string
+        enum:
+          - EFO:0030069
+          - EFO:0020073
+          - EFO:0030068
+          - EFO:0030067
+          - EFO:0030064
+          - EFO:0030070
+          - EFO:0030071
+          - EFO:0030072
diff --git a/schema/cat-vrs/def/CategoricalVariant.rst b/schema/cat-vrs/def/CategoricalVariant.rst
@@ -1,12 +1,11 @@
 
-.. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
-    the :ref:`maturity-model`.
+.. note:: This data class is at a **trial use** maturity level and may change
+    in future releases. Maturity levels are described in the :ref:`maturity-model`.
 
 
 **Computational Definition**
 
-A representation of a categorically-defined domain for variation, in which individual contextual variation instances may be members of the domain.
+A representation of a categorically-defined domain for variation, in which individual Constraintual variation instances may be members of the domain.
 
 **Information Model**
 
@@ -49,7 +48,7 @@ Some CategoricalVariant attributes are inherited from :ref:`gks-core:Entity`.
    *  - members
       - :ref:`Variation` | :ref:`IRI`
       - 0..m
-      - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.
+      - A non-exhaustive list of VRS variation Constraints that satisfy the constraints of this categorical variant.
    *  - constraints
       - :ref:`Constraint`
       - 0..m

diff --git a/schema/cat-vrs/def/Constraint.rst b/schema/cat-vrs/def/Constraint.rst
@@ -1,7 +1,6 @@
 
-.. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
-    the :ref:`maturity-model`.
+.. note:: This data class is at a **trial use** maturity level and may change
+    in future releases. Maturity levels are described in the :ref:`maturity-model`.
 
 
 **Computational Definition**

diff --git a/schema/cat-vrs/def/CopyChangeConstraint.rst b/schema/cat-vrs/def/CopyChangeConstraint.rst
diff --git a/schema/cat-vrs/def/CopyConstraint.rst b/schema/cat-vrs/def/CopyConstraint.rst
@@ -0,0 +1,35 @@
+
+.. note:: This data class is at a **trial use** maturity level and may change
+    in future releases. Maturity levels are described in the :ref:`maturity-model`.
+
+
+**Computational Definition**
+
+The quantity of copies or the type of copy change that a member of this categorical variant must have. One and only one MUST be specified.
+
+**Information Model**
+
+Some CopyConstraint attributes are inherited from :ref:`Constraint`.
+
+.. list-table::
+   :class: clean-wrap
+   :header-rows: 1
+   :align: left
+   :widths: auto
+
+   *  - Field
+      - Type
+      - Limits
+      - Description
+   *  - type
+      - string
+      - 1..1
+      - MUST be "CopyConstraint"
+   *  - copies
+      - integer | :ref:`Range`
+      - 0..1
+      - The precise value or range of copies a member of this categorical variant must have.
+   *  - copyChange
+      - string
+      - 0..1
+      - The type of copy change a member of this categorical variant must have.
diff --git a/schema/cat-vrs/def/CopyCountConstraint.rst b/schema/cat-vrs/def/CopyCountConstraint.rst