add CNV profile

ga4gh · Sep 9, 2024 · 3df5dcd · 3df5dcd
1 parent 82ac4c7
commit 3df5dcd
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Showing 10 changed files with 137 additions and 8 deletions.
diff --git a/schema/cat-vrs/profiles/cat-vrs-profiles-source.yaml b/schema/cat-vrs/profiles/cat-vrs-profiles-source.yaml
@@ -14,7 +14,7 @@ $defs:
     type: object
     maturity: draft
     description: >-
-      Categorical Variant constraints found in Protein Sequence Consequences.
+      Cat-VRS Constraints found in Protein Sequence Consequences.
     properties:
       constraints:
         contains:
@@ -41,7 +41,7 @@ $defs:
     type: object
     maturity: draft
     description: >-
-      Categorical Variant constraints found in Canonical Alleles.
+      Cat-VRS Constraints found in Canonical Alleles.
     properties:
       constraints:
         contains:
@@ -65,4 +65,33 @@ $defs:
       across different genome assemblies and associated cDNA transcript representations.
     allOf:
       - $ref: "#/$defs/CanonicalAlleleProperties"
+      - $ref: "/ga4gh/schema/cat-vrs/1.x/core/json/CategoricalVariant"
+
+  CategoricalCnvProperties:
+    type: object
+    maturity: draft
+    description: >-
+      Cat-VRS Constraints found in CategoricalCnvs.
+    properties:
+      constraints:
+        allOf:
+          - contains:
+              allOf:
+                - $ref: "/ga4gh/schema/cat-vrs/1.x/core/json/DefiningContextConstraint"
+                - type: object
+                  properties:
+                    relations:
+                      contains:
+                        const: sequence_liftover
+          - contains:
+              anyOf:
+                - $ref: "/ga4gh/schema/cat-vrs/1.x/core/json/CopyCountConstraint"
+                - $ref: "/ga4gh/schema/cat-vrs/1.x/core/json/CopyChangeConstraint"
+
+  CategoricalCnv:
+    maturity: draft
+    description: >-
+      A representation of the constraints for matching knowledge about CNVs.
+    allOf:
+      - $ref: "#/$defs/CategoricalCnvProperties"
       - $ref: "/ga4gh/schema/cat-vrs/1.x/core/json/CategoricalVariant"
diff --git a/schema/cat-vrs/profiles/def/CanonicalAlleleProperties.rst b/schema/cat-vrs/profiles/def/CanonicalAlleleProperties.rst
@@ -1,6 +1,6 @@
 **Computational Definition**
 
-Categorical Variant constraints found in Canonical Alleles.
+Cat-VRS Constraints found in Canonical Alleles.
 
 **Information Model**
 

diff --git a/schema/cat-vrs/profiles/def/CategoricalCnv.rst b/schema/cat-vrs/profiles/def/CategoricalCnv.rst
@@ -0,0 +1,17 @@
+**Computational Definition**
+
+A representation of the constraints for matching knowledge about CNVs.
+
+**Information Model**
+
+
+.. list-table::
+   :class: clean-wrap
+   :header-rows: 1
+   :align: left
+   :widths: auto
+
+   *  - Field
+      - Type
+      - Limits
+      - Description
diff --git a/schema/cat-vrs/profiles/def/CategoricalCnvProperties.rst b/schema/cat-vrs/profiles/def/CategoricalCnvProperties.rst
@@ -0,0 +1,21 @@
+**Computational Definition**
+
+Cat-VRS Constraints found in CategoricalCnvs.
+
+**Information Model**
+
+
+.. list-table::
+   :class: clean-wrap
+   :header-rows: 1
+   :align: left
+   :widths: auto
+
+   *  - Field
+      - Type
+      - Limits
+      - Description
+   *  - constraints
+      - _Not Specified_
+      - 0..1
+      - 
diff --git a/schema/cat-vrs/profiles/def/ProteinSequenceConsequenceProperties.rst b/schema/cat-vrs/profiles/def/ProteinSequenceConsequenceProperties.rst
@@ -1,6 +1,6 @@
 **Computational Definition**
 
-Categorical Variant constraints found in Protein Sequence Consequences.
+Cat-VRS Constraints found in Protein Sequence Consequences.
 
 **Information Model**
 

diff --git a/schema/cat-vrs/profiles/json/CanonicalAlleleProperties b/schema/cat-vrs/profiles/json/CanonicalAlleleProperties
@@ -4,7 +4,7 @@
    "title": "CanonicalAlleleProperties",
    "type": "object",
    "maturity": "draft",
-   "description": "Categorical Variant constraints found in Canonical Alleles.",
+   "description": "Cat-VRS Constraints found in Canonical Alleles.",
    "properties": {
       "constraints": {
          "contains": {

diff --git a/schema/cat-vrs/profiles/json/CategoricalCnv b/schema/cat-vrs/profiles/json/CategoricalCnv
@@ -0,0 +1,16 @@
+{
+   "$schema": "https://json-schema.org/draft/2020-12/schema",
+   "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/profiles/json/CategoricalCnv",
+   "title": "CategoricalCnv",
+   "type": "object",
+   "maturity": "draft",
+   "description": "A representation of the constraints for matching knowledge about CNVs.",
+   "allOf": [
+      {
+         "$ref": "/ga4gh/schema/cat-vrs/1.x/profiles/json/CategoricalCnvProperties"
+      },
+      {
+         "$ref": "/ga4gh/schema/cat-vrs/1.x/core/json/CategoricalVariant"
+      }
+   ]
+}
diff --git a/schema/cat-vrs/profiles/json/CategoricalCnvProperties b/schema/cat-vrs/profiles/json/CategoricalCnvProperties
@@ -0,0 +1,46 @@
+{
+   "$schema": "https://json-schema.org/draft/2020-12/schema",
+   "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/profiles/json/CategoricalCnvProperties",
+   "title": "CategoricalCnvProperties",
+   "type": "object",
+   "maturity": "draft",
+   "description": "Cat-VRS Constraints found in CategoricalCnvs.",
+   "properties": {
+      "constraints": {
+         "allOf": [
+            {
+               "contains": {
+                  "allOf": [
+                     {
+                        "$ref": "/ga4gh/schema/cat-vrs/1.x/core/json/DefiningContextConstraint"
+                     },
+                     {
+                        "type": "object",
+                        "properties": {
+                           "relations": {
+                              "contains": {
+                                 "const": "sequence_liftover"
+                              }
+                           }
+                        }
+                     }
+                  ]
+               }
+            },
+            {
+               "contains": {
+                  "anyOf": [
+                     {
+                        "$ref": "/ga4gh/schema/cat-vrs/1.x/core/json/CopyCountConstraint"
+                     },
+                     {
+                        "$ref": "/ga4gh/schema/cat-vrs/1.x/core/json/CopyChangeConstraint"
+                     }
+                  ]
+               }
+            }
+         ]
+      }
+   },
+   "required": []
+}
diff --git a/schema/cat-vrs/profiles/json/ProteinSequenceConsequenceProperties b/schema/cat-vrs/profiles/json/ProteinSequenceConsequenceProperties
@@ -4,7 +4,7 @@
    "title": "ProteinSequenceConsequenceProperties",
    "type": "object",
    "maturity": "draft",
-   "description": "Categorical Variant constraints found in Protein Sequence Consequences.",
+   "description": "Cat-VRS Constraints found in Protein Sequence Consequences.",
    "properties": {
       "constraints": {
          "contains": {

diff --git a/tests/test_definitions.yaml b/tests/test_definitions.yaml
@@ -6,6 +6,6 @@ tests:
   - test_file: describedVariant-ex1.yaml
     definition: CategoricalVariant
   - test_file: categoricalCnv-ex1.yaml
-    definition: CategoricalVariant
+    definition: CategoricalCnv
   - test_file: categoricalCnv-ex2.yaml
-    definition: CategoricalVariant
+    definition: CategoricalCnv