building quantiy change category

docs/source/getting_involved.rst

@@ -7,9 +7,9 @@ Cat-VRS is driven by community involvement. This product is early in development
 can get involved:
 
 
-* `Join the group in GA4GH to get regular updates on our progress.<https://www.ga4gh.org/get-involved/join-our-community/join/>`_
+* `Join the group in GA4GH to get regular updates on our progress. <https://www.ga4gh.org/get-involved/join-our-community/join/>`_
 
-* Twice-monthly meetings.  The schedule for the next meeting can be found `on the CatVar website in GA4GH.<https://www.ga4gh.org/product/categorical-variation-catvar/>`_  Scroll to the bottom and click on "Meetings"  Currently the Categorical Variation Working Group meets every month on the 1st Wednesday from 20:00-21:00 UTC and the 3rd Tuesday from 13:00 - 14:00 UTC, to allow for participation from collaborators across the globe.
+* Twice-monthly meetings.  The schedule for the next meeting can be found `on the CatVar website in GA4GH. <https://www.ga4gh.org/product/categorical-variation-catvar/>`_  Scroll to the bottom and click on "Meetings"  Currently the Categorical Variation Working Group meets every month on the 1st Wednesday from 20:00-21:00 UTC and the 3rd Tuesday from 13:00 - 14:00 UTC, to allow for participation from collaborators across the globe.
 
 * Slack `#GKS-categorical-variation channel. <https://ga4gh.slack.com/archives/C05UKK8DML7>`_
 

schema/catvrs/catvrs-source.yaml

@@ -174,6 +174,122 @@ $defs:
     required:
       - label
 
+  # QuantityChange:
+  #   maturity: draft
+  #   type: object
+  #   inherits: CategoricalVariation
+  #   description: >-
+  #     The Quantity Change class captures one axis of variation in the generalized model of categorical
+  #     variation.  It is used to model quantitative measure changes in a given biological level of
+  #     variation.
+  #   properties:
+  #     type:
+  #       type: string
+  #       const: QuantityChange
+  #       default: QuantityChange
+  #       description: 'MUST be "QuantityChange"'
+  #     label:
+  #       extends: label
+  #       description: >-
+  #         A primary label for the categorical variation. This required property should provide a 
+  #         short and descriptive textual representation of the concept.
+  #     description:
+  #       extends: description
+  #       description: >-
+  #         A textual description of the domain of variation that should match the categorical 
+  #         variation entity.
+  #     locationMatchCharacteristic:
+  #       type: string
+  #       enum: ['exact', 'partial', 'subinterval', 'superinterval']
+  #       description: >-
+  #         The characteristics of a valid match between a contextual CNV location (the query) and the 
+  #         Categorical CNV location (the domain), when both query and domain are represented on the same 
+  #         reference sequence. An `exact` match requires the location of the query and domain to be identical. 
+  #         A `subinterval` match requires the query to be a subinterval of the domain. A `superinterval` match
+  #         requires the query to be a superinterval of the domain. A `partial` match requires at least 1 residue
+  #         of overlap between the query and domain.
+  #     copyChange:
+  #       type: string
+  #       enum: [ "efo:0030069", "efo:0020073", "efo:0030068", "efo:0030067", "efo:0030064", "efo:0030070", "efo:0030071", "efo:0030072" ]
+  #       description: >-
+  #         A representation of the change in copies of a sequence in a system. 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).
+  #     copies:
+  #       oneOf:
+  #         - type: integer
+  #         - $refCurie: vrs:Range
+  #       description: >-
+  #         The integral number of copies of the subject in a system.
+  #   required:
+  #     - label
+
+  NumberCount:
+    maturity: draft
+    ga4ghDigest:
+      keys:
+        - copies
+    type: object
+    description: >-
+      The absolute count of a discrete assayable unit (e.g. chromosome, gene, or sequence).
+    properties:
+      type:
+        type: string
+        const: "NumberCount"
+        default: "NumberCount"
+        description: >-
+          MUST be "NumberCount"
+      copies:
+        oneOf:
+          - type: integer
+          - $refCurie: vrs:Range
+        description: >-
+          The integral quantity of the subject in a system
+    required: [ "copies" ]
+
+
+
+
+
+  # # Categorical Variation is presented top-down. Everything rolls up to
+  # # CategoricalVariant, is composed of one or several level variants, 
+  # # each of which is in turn associated with a biological level of 
+  # # variation, and relevant properties to intensionally define set
+  # # membership.
+
+  # # =============================================================================
+  # # Top-level Categorical Variation concepts
+  # # =============================================================================
+
+  # CategoricalVariant:
+  #   inherits: gks.core:DomainEntity
+  #   description: >-
+  #     A top-level representation of a categorically-defined domain for variation across one or multiple biological levels in which individual contextual variants may be members of the domain.
+  #   properties:
+  #     id:
+  #       type: string
+  #       description: >-
+  #         The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is 
+  #         unique within a given system. The identified entity may have a different 'id' in a different 
+  #         system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE).
+  #     label:
+  #       type: string
+  #       description: A primary label for the entity.
+  #     description:
+  #       type: string
+  #       description: A free-text description of the entity.
+  #     extensions:
+  #       type: array
+  #       ordered: true
+  #       items:
+  #         - $refExtension: gks.core:Extension
+
+
+
+
+
+
 #  CanonicalLocation:
 #    inherits: Constraint
 #    type: object

schema/catvrs/def/NumberCount.rst

@@ -0,0 +1,24 @@
+**Computational Definition**
+
+The absolute count of a discrete assayable unit (e.g. chromosome, gene, or sequence).
+
+    **Information Model**
+
+    .. list-table::
+       :class: clean-wrap
+       :header-rows: 1
+       :align: left
+       :widths: auto
+
+       *  - Field
+          - Type
+          - Limits
+          - Description
+       *  - type
+          - string
+          - 0..1
+          - MUST be "NumberCount"
+       *  - copies
+          - integer | `Range <../vrs/vrs.yaml#/$defs/Range>`_
+          - 1..1
+          - The integral quantity of the subject in a system

schema/catvrs/json/NumberCount

@@ -0,0 +1,36 @@
+{
+   "$schema": "https://json-schema.org/draft/2020-12/schema",
+   "$id": "https://w3id.org/ga4gh/schema/catvrs/1.x/json/NumberCount",
+   "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": {
+         "type": "string",
+         "const": "NumberCount",
+         "default": "NumberCount",
+         "description": "MUST be \"NumberCount\""
+      },
+      "copies": {
+         "oneOf": [
+            {
+               "$ref": "/ga4gh/schema/vrs/2.x/json/Range"
+            },
+            {
+               "type": "integer"
+            }
+         ],
+         "description": "The integral quantity of the subject in a system"
+      }
+   },
+   "required": [
+      "copies"
+   ],
+   "additionalProperties": false
+}