* embed *Properties into recipes

* refine DefiningContext to DefiningAllele & DefiningLocation * redraft CategoricalCnv on recent design changes
ga4gh · Nov 5, 2024 · f919266 · f919266
1 parent 157a0c8
commit f919266
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diff --git a/examples/canonicalAllele-ex1.yaml b/examples/canonicalAllele-ex1.yaml
@@ -2,8 +2,8 @@ id: clinvar:662001
 label: NM_004958.4(MTOR):c.5992_5993del (p.Met1998fs)
 type: CategoricalVariant
 constraints:
-  - type: DefiningContextConstraint
-    definingContext:
+  - type: DefiningAlleleContext
+    allele:
       id: ga4gh:VA.PN-6_l2_yI1UPBRCtFnWkR52iZXKVJ8b
       type: Allele
       digest: PN-6_l2_yI1UPBRCtFnWkR52iZXKVJ8b
@@ -42,8 +42,8 @@ constraints:
         - name: clinvar hgvs type
           value: genomic, top-level    
     relations:
-      - sequence_liftover
-      - transcript_projection
+      - liftover_to
+      - transcribes_to
 mappings:
   - coding:
       code: CA915941124

diff --git a/examples/categoricalCnv-ex1.yaml b/examples/categoricalCnv-ex1.yaml
@@ -4,8 +4,8 @@ label: GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3
 constraints:
   - type: CopyCountConstraint
     copies: 3
-  - type: DefiningContextConstraint
-    definingContext:
+  - type: DefiningLocationContext
+    location:
       type: SequenceLocation
       start: [null, 5945462]
       end: [6053792, null]
@@ -14,6 +14,9 @@ constraints:
         type: SequenceReference
         refgetAccession: SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO
         residueAlphabet: na
+    relations:
+      - liftover_to
+    matchCharacteristic: exact
 extensions: 
   - name: vrs processing errors
     value: "NC_000007.14:g.(?_5905831)_(6014161_?)dup: char 26: expected one of '=', 'con', 'copy', 'del', 'dup', 'ins', or 'inv'"

diff --git a/examples/categoricalCnv-ex2.yaml b/examples/categoricalCnv-ex2.yaml
@@ -7,8 +7,8 @@ constraints:
       system: https://www.ebi.ac.uk/ols4/search?ontology=efo&q=
       code: EFO:0030070
       label: Copy Number Gain
-  - type: DefiningContextConstraint
-    definingContext:
+  - type: DefiningLocationContext
+    location:
       type: SequenceLocation
       start: [null, 5945462]
       end: [6053792, null]
@@ -17,6 +17,9 @@ constraints:
         type: SequenceReference
         refgetAccession: SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO
         residueAlphabet: na
+    relations:
+      - liftover_to
+    matchCharacteristic: exact
 extensions: 
   - name: vrs processing errors
     value: "NC_000007.14:g.(?_5905831)_(6014161_?)dup: char 26: expected one of '=', 'con', 'copy', 'del', 'dup', 'ins', or 'inv'"

diff --git a/examples/proteinSequenceConsequence-ex1.yaml b/examples/proteinSequenceConsequence-ex1.yaml
@@ -11,8 +11,8 @@ description: >-
   treating patients that failed to respond to earlier generation TKI therapies.
 label: EGFR L858R
 constraints:
-  - type: "DefiningContextConstraint"
-    definingContext: vrs.json#/ga4gh:VA.kgjrhgf84CEndyLjKdAO0RxN-e3pJjxA
+  - type: "DefiningAlleleContext"
+    allele: vrs.json#/ga4gh:VA.kgjrhgf84CEndyLjKdAO0RxN-e3pJjxA
 members:
   - vrs.json#/ga4gh:VA.7jX7fHgVEqx4C4jMRyZOH0ZBHnLn7_gJ
   - vrs.json#/ga4gh:VA.3_FsKSUHEdurPIw5gqpw6g0_Ga0TEXQh

diff --git a/schema/cat-vrs/cat-vrs-source.yaml b/schema/cat-vrs/cat-vrs-source.yaml
@@ -16,7 +16,7 @@ $defs:
 
   CategoricalVariant:
     type: object
-    inherits: gks-core:DomainEntity
+    inherits: gks-core:Entity
     maturity: draft
     description: >-
       A representation of a categorically-defined domain for variation, in which individual
@@ -42,6 +42,14 @@ $defs:
         ordered: false
         items:
           $ref: "#/$defs/Constraint"
+      mappings:
+        type: array
+        ordered: false
+        items:
+          $ref: "/ga4gh/schema/gks-core/1.x/json/ConceptMapping"
+        description: >-
+          A list of mappings to concepts in terminologies or code systems. Each mapping should
+          include a coding and a relation.
 
   # =============================================================================
   # Constraint Definitions
@@ -52,7 +60,8 @@ $defs:
     description: >-
       Constraints are used to construct an intensional semantics of categorical variant types.
     oneOf:
-      - $ref: "#/$defs/DefiningContextConstraint"
+      - $ref: "#/$defs/DefiningAlleleContext"
+      - $ref: "#/$defs/DefiningLocationContext"
       - $ref: "#/$defs/CopyCountConstraint"
       - $ref: "#/$defs/CopyChangeConstraint"
     heritableProperties:
@@ -61,41 +70,91 @@ $defs:
     heritableRequired:
       - type
 
-  DefiningContextConstraint:
+  DefiningAlleleContext:
+    maturity: draft
+    type: object
+    inherits: Constraint
+    description: >-
+      The defining allele and its associated relationships that are congruent
+      with member variants.
+    properties:
+      type:
+        extends: type
+        const: DefiningAlleleContext
+        default: DefiningAlleleContext
+        description: 'MUST be "DefiningAlleleContext"'
+      allele:
+        oneOf:
+          - $ref: /ga4gh/schema/vrs/2.x/json/Allele
+          - $ref: /ga4gh/schema/gks-core/1.x/json/IRI
+      relations:
+        type: array
+        ordered: false
+        items:
+          type: string
+          enum:
+            - translates_from
+            - translates_from_reading_frame
+            - liftover_to
+            - transcribes_to
+            - translates_to
+            - translates_through
+        description: >-
+          Defined relationships from which members relate to the defining context.
+          ``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
     type: object
     inherits: Constraint
     description: >-
-      The location or location-state, congruent with other reference sequences,
-      about which categorical variation is being described.
+      The defining location and its associated relationships that are congruent
+      with member locations.
     properties:
       type:
         extends: type
-        const: DefiningContextConstraint
-        default: DefiningContextConstraint
-        description: 'MUST be "DefiningContextConstraint"'
-      definingContext:
+        const: DefiningLocationContext
+        default: DefiningLocationContext
+        description: 'MUST be "DefiningLocationContext"'
+      location:
         oneOf:
-          - $ref: /ga4gh/schema/vrs/2.x/json/Variation
-          - $ref: /ga4gh/schema/vrs/2.x/json/Location
+          - $ref: /ga4gh/schema/vrs/2.x/json/SequenceLocation
           - $ref: /ga4gh/schema/gks-core/1.x/json/IRI
       relations:
         type: array
         ordered: false
         items:
           type: string
           enum:
-            - sequence_liftover
-            - transcript_projection
-            - codon_translation
+            - translates_from
+            - translates_from_reading_frame
+            - liftover_to
+            - transcribes_to
+            - translates_to
+            - translates_through
         description: >-
-          Defined relationships between members of the categorical variant and the defining context.
+          Defined relationships from which members relate to the defining context.
           ``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.
+      matchCharacteristic:
+        type: string
+        description: >-
+          A characteristic of the location that is used to match the defining location to member locations. 
+        enum:
+          - exact
+          - encompass
+          - within
+          - overlap
     required:
-      - definingContext
+      - location
+      - matchCharacteristic
 
   CopyCountConstraint:
     maturity: draft

diff --git a/schema/cat-vrs/def/CanonicalAlleleProperties.rst b/schema/cat-vrs/def/CanonicalAlleleProperties.rst
diff --git a/schema/cat-vrs/def/CategoricalCnvProperties.rst b/schema/cat-vrs/def/CategoricalCnvProperties.rst
diff --git a/schema/cat-vrs/def/CategoricalVariant.rst b/schema/cat-vrs/def/CategoricalVariant.rst
@@ -10,7 +10,7 @@ A representation of a categorically-defined domain for variation, in which indiv
 
 **Information Model**
 
-Some CategoricalVariant attributes are inherited from :ref:`gks-core:DomainEntity`.
+Some CategoricalVariant attributes are inherited from :ref:`gks-core:Entity`.
 
 .. list-table::
    :class: clean-wrap
@@ -42,10 +42,6 @@ Some CategoricalVariant attributes are inherited from :ref:`gks-core:DomainEntit
       - :ref:`Extension`
       - 0..m
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
-   *  - mappings
-      - :ref:`ConceptMapping`
-      - 0..m
-      - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.
    *  - type
       - string
       - 1..1
@@ -58,3 +54,7 @@ Some CategoricalVariant attributes are inherited from :ref:`gks-core:DomainEntit
       - :ref:`Constraint`
       - 0..m
       - 
+   *  - mappings
+      - :ref:`ConceptMapping`
+      - 0..m
+      - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.
diff --git a/schema/cat-vrs/def/DefiningAlleleContext.rst b/schema/cat-vrs/def/DefiningAlleleContext.rst
@@ -0,0 +1,36 @@
+
+.. 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`.
+
+
+**Computational Definition**
+
+The defining allele and its associated relationships that are congruent with member variants.
+
+**Information Model**
+
+Some DefiningAlleleContext 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 "DefiningAlleleContext"
+   *  - allele
+      - :ref:`Allele` | :ref:`IRI`
+      - 1..1
+      - 
+   *  - relations
+      - string
+      - 0..m
+      - Defined relationships from which members relate to the defining context. ``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.
diff --git a/schema/cat-vrs/def/DefiningContextConstraint.rst b/schema/cat-vrs/def/DefiningContextConstraint.rst