added copyChange class

ga4gh · Mar 27, 2024 · f87c702 · f87c702
1 parent ee4062c
commit f87c702
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Showing 5 changed files with 108 additions and 13 deletions.
diff --git a/schema/catvrs/catvrs-source.yaml b/schema/catvrs/catvrs-source.yaml
@@ -227,9 +227,9 @@ $defs:
 
   NumberCount:
     maturity: draft
-    ga4ghDigest:
-      keys:
-        - copies
+    # ga4ghDigest:
+    #   keys:
+    #     - numberCount
     type: object
     description: >-
       The absolute count of a discrete assayable unit (e.g. chromosome, gene, or sequence).
@@ -240,15 +240,45 @@ $defs:
         default: "NumberCount"
         description: >-
           MUST be "NumberCount"
-      copies:
+      count:
         oneOf:
           - type: integer
           - $refCurie: vrs:Range
         description: >-
           The integral quantity of the subject in a system
-    required: [ "copies" ]
+    required: [ "count" ]
 
 
+  NumberChange:
+    maturity: draft
+    # ga4ghDigest:
+    #   keys:
+    #     - numberChange
+    #   prefix: CX
+    type: object
+    description: >-
+      A quantitative assessment of a unit within a system (e.g. genome, cell,
+      etc.) relative to a baseline quantity.
+    properties:
+      type:
+        type: string
+        const: "NumberChange"
+        default: "NumberChange"
+        description: >-
+          MUST be "NumberChange"
+      change:
+        oneOf:
+          - type: integer
+          - $refCurie: vrs:Range
+          - copyChange:
+            type: string
+            enum: [ "efo:0030069", "efo:0020073", "efo:0030068", "efo:0030067", "efo:0030064", "efo:0030070",
+                    "efo:0030071", "efo:0030072" ]
+            description: >-
+              MUST be one of "efo:0030069" (complete genomic loss), "efo:0020073" (high-level loss),
+              "efo:0030068" (low-level loss), "efo:0030067" (loss), "efo:0030064" (regional base ploidy),
+              "efo:0030070" (gain), "efo:0030071" (low-level gain), "efo:0030072" (high-level gain).
+        required: [ "change" ]
 
 
 

diff --git a/schema/catvrs/def/NumberChange.rst b/schema/catvrs/def/NumberChange.rst
@@ -0,0 +1,24 @@
+**Computational Definition**
+
+A quantitative assessment of a unit within a system (e.g. genome, cell, etc.) relative to a baseline quantity.
+
+    **Information Model**
+
+    .. list-table::
+       :class: clean-wrap
+       :header-rows: 1
+       :align: left
+       :widths: auto
+
+       *  - Field
+          - Type
+          - Limits
+          - Description
+       *  - type
+          - string
+          - 0..1
+          - MUST be "NumberChange"
+       *  - change
+          - integer | `Range <../vrs/vrs.yaml#/$defs/Range>`_ | string
+          - 0..1
+          - 
diff --git a/schema/catvrs/def/NumberCount.rst b/schema/catvrs/def/NumberCount.rst
@@ -18,7 +18,7 @@ The absolute count of a discrete assayable unit (e.g. chromosome, gene, or seque
           - string
           - 0..1
           - MUST be "NumberCount"
-       *  - copies
+       *  - count
           - integer | `Range <../vrs/vrs.yaml#/$defs/Range>`_
           - 1..1
           - The integral quantity of the subject in a system
diff --git a/schema/catvrs/json/NumberChange b/schema/catvrs/json/NumberChange
@@ -0,0 +1,46 @@
+{
+   "$schema": "https://json-schema.org/draft/2020-12/schema",
+   "$id": "https://w3id.org/ga4gh/schema/catvrs/1.x/json/NumberChange",
+   "title": "NumberChange",
+   "type": "object",
+   "maturity": "draft",
+   "description": "A quantitative assessment of a unit within a system (e.g. genome, cell, etc.) relative to a baseline quantity.",
+   "properties": {
+      "type": {
+         "type": "string",
+         "const": "NumberChange",
+         "default": "NumberChange",
+         "description": "MUST be \"NumberChange\""
+      },
+      "change": {
+         "oneOf": [
+            {
+               "$ref": "/ga4gh/schema/vrs/2.x/json/Range"
+            },
+            {
+               "type": "integer"
+            },
+            {
+               "copyChange": null,
+               "type": "string",
+               "enum": [
+                  "efo:0030069",
+                  "efo:0020073",
+                  "efo:0030068",
+                  "efo:0030067",
+                  "efo:0030064",
+                  "efo:0030070",
+                  "efo:0030071",
+                  "efo:0030072"
+               ],
+               "description": "MUST be one of \"efo:0030069\" (complete genomic loss), \"efo:0020073\" (high-level loss), \"efo:0030068\" (low-level loss), \"efo:0030067\" (loss), \"efo:0030064\" (regional base ploidy), \"efo:0030070\" (gain), \"efo:0030071\" (low-level gain), \"efo:0030072\" (high-level gain)."
+            }
+         ],
+         "required": [
+            "change"
+         ]
+      }
+   },
+   "required": [],
+   "additionalProperties": false
+}
diff --git a/schema/catvrs/json/NumberCount b/schema/catvrs/json/NumberCount
@@ -4,11 +4,6 @@
    "title": "NumberCount",
    "type": "object",
    "maturity": "draft",
-   "ga4ghDigest": {
-      "keys": [
-         "copies"
-      ]
-   },
    "description": "The absolute count of a discrete assayable unit (e.g. chromosome, gene, or sequence).",
    "properties": {
       "type": {
@@ -17,7 +12,7 @@
          "default": "NumberCount",
          "description": "MUST be \"NumberCount\""
       },
-      "copies": {
+      "count": {
          "oneOf": [
             {
                "$ref": "/ga4gh/schema/vrs/2.x/json/Range"
@@ -30,7 +25,7 @@
       }
    },
    "required": [
-      "copies"
+      "count"
    ],
    "additionalProperties": false
 }