#98: Adding FeatureContextConstraint (#108)

* Reimplemented FeatureContextConstraint, other branch got very messy when rebasing post- merge of commit 11848ce / pull request 102

* Added empty line at end of cat-vrs-source.yaml

* Added compiled schema def and json files that were missed in pull request 102. I believe these not being committed were why tests were failing through github actions.

* Ran pre-commit hook locally, which fixed trailing whitepsace errors

docs/source/concepts/catvrs_model.rst

@@ -54,3 +54,8 @@ CopyChangeConstraint
 ####################
 
 .. include:: ../def/cat-vrs/CopyChangeConstraint.rst
+
+FeatureContextConstraint
+########################
+
+.. include:: ../def/cat-vrs/FeatureContextConstraint.rst

examples/proteinMarker-ex1.yaml

@@ -0,0 +1,25 @@
+id: pr:p03372
+type: CategoricalVariant
+description: >-
+  An estrogen receptor that is encoded in the genome of human.
+label: Estrogen receptor
+constraints:
+  - type: FeatureContextConstraint
+    featureContext:
+      id: pr:p03372
+      conceptType: Protein
+      label: Estrogen receptor
+      primaryCode: hgnc:3236
+      mappings:
+        - coding:
+            system: https://proconsortium.org
+            code: pr:p03372
+          relation: exactMatch
+        - coding:
+            system: https://www.uniprot.org
+            code: p03372
+          relation: relatedMatch
+        - coding:
+            system: https://www.genenames.org
+            code: hgnc:3467
+          relation: relatedMatch

examples/proteinSequenceConsequence-ex1.yaml

@@ -15,6 +15,30 @@ constraints:
     allele: vrs.json#/ga4gh:VA.kgjrhgf84CEndyLjKdAO0RxN-e3pJjxA
     relations:
       - primaryCode: translates_from
+  - type: FeatureContextConstraint
+    featureContext:
+      id: normalize.gene.hgnc:3236
+      extensions:
+        - name: symbol_status
+          value: approved
+        - name: approved_name
+          value: epidermal growth factor receptor
+      conceptType: Gene
+      name: EGFR
+      primaryCode: hgnc:3236
+      mappings:
+        - coding:
+            system: https://www.genenames.org
+            code: hgnc:3236
+          relation: exactMatch
+        - coding:
+            system: https://www.ensembl.org
+            code: ensembl:ENSG00000146648
+          relation: relatedMatch
+        - coding:
+            system: https://www.ncbi.nlm.nih.gov/gene/
+            code: ncbigene:1956
+          relation: relatedMatch
 members:
   - vrs.json#/ga4gh:VA.7jX7fHgVEqx4C4jMRyZOH0ZBHnLn7_gJ
   - vrs.json#/ga4gh:VA.3_FsKSUHEdurPIw5gqpw6g0_Ga0TEXQh

schema/cat-vrs/cat-vrs-source.yaml

@@ -68,6 +68,7 @@ $defs:
       - $ref: "#/$defs/DefiningLocationConstraint"
       - $ref: "#/$defs/CopyCountConstraint"
       - $ref: "#/$defs/CopyChangeConstraint"
+      - $ref: "#/$defs/FeatureContextConstraint"
     heritableProperties:
       type:
         type: string
@@ -185,3 +186,21 @@ $defs:
           - EFO:0030072
     required:
       - copyChange
+
+  FeatureContextConstraint:
+    maturity: draft
+    type: object
+    inherits: Constraint
+    description: >-
+      The feature that members of this categorical variant are associated with.
+    properties:
+      type:
+        extends: type
+        const: FeatureContextConstraint
+        default: FeatureContextConstraint
+        description: 'MUST be "FeatureContextConstraint"'
+      featureContext:
+        description: A feature identifier.
+        $refCurie: gks.core:MappableConcept
+    required:
+      - featureContext

schema/cat-vrs/def/FeatureContextConstraint.rst

@@ -0,0 +1,33 @@
+.. 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 feature that members of this categorical variant are associated with.
+
+**Information Model**
+
+Some FeatureContextConstraint attributes are inherited from :ref:`Constraint`.
+
+.. list-table::
+   :class: clean-wrap
+   :header-rows: 1
+   :align: left
+   :widths: auto
+
+   *  - Field
+      - Flags
+      - Type
+      - Limits
+      - Description
+   *  - type
+      -
+      - string
+      - 1..1
+      - MUST be "FeatureContextConstraint"
+   *  - featureContext
+      -
+      - :ref:`MappableConcept`
+      - 1..1
+      - A feature identifier.

schema/cat-vrs/json/CategoricalVariant

@@ -74,6 +74,9 @@
                },
                {
                   "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningLocationConstraint"
+               },
+               {
+                  "$ref": "/ga4gh/schema/cat-vrs/1.x/json/FeatureContextConstraint"
                }
             ]
          }

schema/cat-vrs/json/Constraint

@@ -17,6 +17,9 @@
       },
       {
          "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningLocationConstraint"
+      },
+      {
+         "$ref": "/ga4gh/schema/cat-vrs/1.x/json/FeatureContextConstraint"
       }
    ]
 }

schema/cat-vrs/json/FeatureContextConstraint

@@ -0,0 +1,25 @@
+{
+   "$schema": "https://json-schema.org/draft/2020-12/schema",
+   "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/FeatureContextConstraint",
+   "title": "FeatureContextConstraint",
+   "type": "object",
+   "maturity": "draft",
+   "description": "The feature that members of this categorical variant are associated with.",
+   "properties": {
+      "type": {
+         "type": "string",
+         "const": "FeatureContextConstraint",
+         "default": "FeatureContextConstraint",
+         "description": "MUST be \"FeatureContextConstraint\""
+      },
+      "featureContext": {
+         "description": "A feature identifier.",
+         "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/MappableConcept"
+      }
+   },
+   "required": [
+      "featureContext",
+      "type"
+   ],
+   "additionalProperties": false
+}