diff --git a/docs/source/images/schema-current.png b/docs/source/images/schema-current.png index 12642399..cd8c58fc 100644 Binary files a/docs/source/images/schema-current.png and b/docs/source/images/schema-current.png differ diff --git a/schema/vrs/def/CopyNumber.rst b/schema/vrs/def/CopyNumber.rst deleted file mode 100644 index b359df9c..00000000 --- a/schema/vrs/def/CopyNumber.rst +++ /dev/null @@ -1,92 +0,0 @@ -.. 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** - -A measure of the copies of a :ref:`Location` within a system (e.g. genome, cell, etc.) - -**GA4GH Digest** - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Prefix - - Keys - - * - None - - ['location', 'type'] - - -**Information Model** - -Some CopyNumber attributes are inherited from :ref:`Variation`. - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Flags - - Type - - Limits - - Description - * - id - - - - string - - 0..1 - - The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another. - * - type - - - - string - - 1..1 - - - * - label - - - - string - - 0..1 - - A primary name for the entity. - * - description - - - - string - - 0..1 - - A free-text description of the Entity. - * - alternativeLabels - - - .. raw:: html - - ⋮ - - string - - 0..m - - Alternative name(s) for the Entity. - * - extensions - - - .. raw:: html - - ⋮ - - :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. - * - digest - - - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. - * - expressions - - - .. raw:: html - - ⋮ - - :ref:`Expression` - - 0..m - - - * - location - - - - :ref:`iriReference` | :ref:`Location` - - 1..1 - - A location for which the number of systemic copies is described. diff --git a/schema/vrs/def/CopyNumberChange.rst b/schema/vrs/def/CopyNumberChange.rst index 910ae111..06950f48 100644 --- a/schema/vrs/def/CopyNumberChange.rst +++ b/schema/vrs/def/CopyNumberChange.rst @@ -23,7 +23,7 @@ An assessment of the copy number of a :ref:`Location` or a :ref:`Gene` within a **Information Model** -Some CopyNumberChange attributes are inherited from :ref:`CopyNumber`. +Some CopyNumberChange attributes are inherited from :ref:`Variation`. .. list-table:: :class: clean-wrap @@ -80,16 +80,16 @@ Some CopyNumberChange attributes are inherited from :ref:`CopyNumber`. - :ref:`Expression` - 0..m - - * - location - - - - :ref:`iriReference` | :ref:`Location` - - 1..1 - - A location for which the number of systemic copies is described. * - type - - string - 1..1 - MUST be "CopyNumberChange" + * - location + - + - :ref:`iriReference` | :ref:`Location` + - 1..1 + - The location of the subject of the copy change. * - copyChange - - :ref:`Coding` diff --git a/schema/vrs/def/CopyNumberCount.rst b/schema/vrs/def/CopyNumberCount.rst index 0dab4a76..3e3e8839 100644 --- a/schema/vrs/def/CopyNumberCount.rst +++ b/schema/vrs/def/CopyNumberCount.rst @@ -1,5 +1,5 @@ -.. warning:: This data class is at a **draft** maturity level and may \ - change significantly in future releases. Maturity \ +.. note:: This data class is at a **trial use** maturity level and may \ + change in future releases. Maturity \ levels are described in the :ref:`maturity-model`. **Computational Definition** @@ -23,7 +23,7 @@ The absolute count of discrete copies of a :ref:`Location` or :ref:`Gene`, withi **Information Model** -Some CopyNumberCount attributes are inherited from :ref:`CopyNumber`. +Some CopyNumberCount attributes are inherited from :ref:`Variation`. .. list-table:: :class: clean-wrap @@ -80,16 +80,16 @@ Some CopyNumberCount attributes are inherited from :ref:`CopyNumber`. - :ref:`Expression` - 0..m - - * - location - - - - :ref:`iriReference` | :ref:`Location` - - 1..1 - - A location for which the number of systemic copies is described. * - type - - string - 1..1 - MUST be "CopyNumberCount" + * - location + - + - :ref:`iriReference` | :ref:`Location` + - 1..1 + - The location of the subject of the copy count. * - copies - - integer | :ref:`Range` diff --git a/schema/vrs/json/CopyNumberChange b/schema/vrs/json/CopyNumberChange index 3e432f68..fe3555f5 100644 --- a/schema/vrs/json/CopyNumberChange +++ b/schema/vrs/json/CopyNumberChange @@ -56,6 +56,12 @@ "$ref": "/ga4gh/schema/vrs/2.x/json/Expression" } }, + "type": { + "type": "string", + "const": "CopyNumberChange", + "default": "CopyNumberChange", + "description": "MUST be \"CopyNumberChange\"" + }, "location": { "oneOf": [ { @@ -65,13 +71,7 @@ "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" } ], - "description": "A location for which the number of systemic copies is described." - }, - "type": { - "type": "string", - "const": "CopyNumberChange", - "default": "CopyNumberChange", - "description": "MUST be \"CopyNumberChange\"" + "description": "The location of the subject of the copy change." }, "copyChange": { "$ref": "/ga4gh/schema/gks-core/1.x/json/Coding", diff --git a/schema/vrs/json/CopyNumberCount b/schema/vrs/json/CopyNumberCount index 3c4fe1b8..4cb72080 100644 --- a/schema/vrs/json/CopyNumberCount +++ b/schema/vrs/json/CopyNumberCount @@ -3,7 +3,7 @@ "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/CopyNumberCount", "title": "CopyNumberCount", "type": "object", - "maturity": "draft", + "maturity": "trial use", "ga4ghDigest": { "keys": [ "copies", @@ -56,6 +56,12 @@ "$ref": "/ga4gh/schema/vrs/2.x/json/Expression" } }, + "type": { + "type": "string", + "const": "CopyNumberCount", + "default": "CopyNumberCount", + "description": "MUST be \"CopyNumberCount\"" + }, "location": { "oneOf": [ { @@ -65,13 +71,7 @@ "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" } ], - "description": "A location for which the number of systemic copies is described." - }, - "type": { - "type": "string", - "const": "CopyNumberCount", - "default": "CopyNumberCount", - "description": "MUST be \"CopyNumberCount\"" + "description": "The location of the subject of the copy count." }, "copies": { "oneOf": [ diff --git a/schema/vrs/vrs-source.yaml b/schema/vrs/vrs-source.yaml index c06e9343..ae327128 100644 --- a/schema/vrs/vrs-source.yaml +++ b/schema/vrs/vrs-source.yaml @@ -191,30 +191,15 @@ $defs: # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # SystemicVariation - CopyNumber: - maturity: draft - ga4ghDigest: - keys: - - location - inherits: SystemicVariation - description: >- - A measure of the copies of a :ref:`Location` within a system (e.g. genome, cell, etc.) - heritableProperties: - location: - oneOf: - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" - - $ref: "#/$defs/Location" - description: >- - A location for which the number of systemic copies is described. - heritableRequired: [ "location" ] - + CopyNumberCount: - maturity: draft + maturity: trial use ga4ghDigest: keys: + - location - copies prefix: CN - inherits: CopyNumber + inherits: SystemicVariation type: object description: >- The absolute count of discrete copies of a :ref:`Location` or :ref:`Gene`, @@ -226,21 +211,28 @@ $defs: default: "CopyNumberCount" description: >- MUST be "CopyNumberCount" + location: + oneOf: + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + - $ref: "#/$defs/Location" + description: >- + The location of the subject of the copy count. copies: oneOf: - type: integer - $ref: "#/$defs/Range" description: >- The integral number of copies of the subject in a system - required: [ "copies" ] + required: [ "location", "copies" ] CopyNumberChange: maturity: draft ga4ghDigest: keys: + - location - copyChange prefix: CX - inherits: CopyNumber + inherits: SystemicVariation type: object description: >- An assessment of the copy number of a :ref:`Location` or a :ref:`Gene` within a system (e.g. genome, cell, @@ -252,13 +244,19 @@ $defs: default: "CopyNumberChange" description: >- MUST be "CopyNumberChange" + location: + oneOf: + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + - $ref: "#/$defs/Location" + description: >- + The location of the subject of the copy change. copyChange: $ref: "/ga4gh/schema/gks-core/1.x/json/Coding" description: >- MUST be a :ref:`Coding` representing 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: [ "copyChange" ] + required: [ "location", "copyChange" ] # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Locations