diff --git a/examples/canonicalAllele-ex1.yaml b/examples/canonicalAllele-ex1.yaml index fbdcc9e..68473f3 100644 --- a/examples/canonicalAllele-ex1.yaml +++ b/examples/canonicalAllele-ex1.yaml @@ -2,7 +2,7 @@ id: clinvar:662001 label: NM_004958.4(MTOR):c.5992_5993del (p.Met1998fs) type: CategoricalVariant constraints: - - type: DefiningAlleleContext + - type: DefiningAlleleConstraint allele: id: ga4gh:VA.PN-6_l2_yI1UPBRCtFnWkR52iZXKVJ8b type: Allele diff --git a/examples/categoricalCnv-ex1.yaml b/examples/categoricalCnv-ex1.yaml index b6a9637..beef54a 100644 --- a/examples/categoricalCnv-ex1.yaml +++ b/examples/categoricalCnv-ex1.yaml @@ -2,9 +2,9 @@ id: clinvar:151061 type: CategoricalVariant label: GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3 constraints: - - type: CopyCountConstraint + - type: CopyConstraint copies: 3 - - type: DefiningLocationContext + - type: DefiningLocationConstraint location: type: SequenceLocation start: [null, 5945462] diff --git a/examples/categoricalCnv-ex2.yaml b/examples/categoricalCnv-ex2.yaml index 114f57d..cfcbcfb 100644 --- a/examples/categoricalCnv-ex2.yaml +++ b/examples/categoricalCnv-ex2.yaml @@ -2,12 +2,9 @@ id: clinvar:151061 type: CategoricalVariant label: GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3 constraints: - - type: CopyChangeConstraint - copyChange: - system: https://www.ebi.ac.uk/ols4/search?ontology=efo&q= - code: EFO:0030070 - label: Copy Number Gain - - type: DefiningLocationContext + - type: CopyConstraint + copyChange: EFO:0030070 + - type: DefiningLocationConstraint location: type: SequenceLocation start: [null, 5945462] diff --git a/examples/proteinSequenceConsequence-ex1.yaml b/examples/proteinSequenceConsequence-ex1.yaml index 91cdda7..1ca7975 100644 --- a/examples/proteinSequenceConsequence-ex1.yaml +++ b/examples/proteinSequenceConsequence-ex1.yaml @@ -11,7 +11,7 @@ description: >- treating patients that failed to respond to earlier generation TKI therapies. label: EGFR L858R constraints: - - type: "DefiningAlleleContext" + - type: DefiningAlleleConstraint allele: vrs.json#/ga4gh:VA.kgjrhgf84CEndyLjKdAO0RxN-e3pJjxA members: - vrs.json#/ga4gh:VA.7jX7fHgVEqx4C4jMRyZOH0ZBHnLn7_gJ diff --git a/schema/cat-vrs/cat-vrs-source.yaml b/schema/cat-vrs/cat-vrs-source.yaml index b4eb2ef..881a5a5 100644 --- a/schema/cat-vrs/cat-vrs-source.yaml +++ b/schema/cat-vrs/cat-vrs-source.yaml @@ -17,10 +17,10 @@ $defs: CategoricalVariant: type: object inherits: gks-core:Entity - maturity: draft + maturity: trial use description: >- A representation of a categorically-defined domain for variation, in which individual - contextual variation instances may be members of the domain. + Constraintual variation instances may be members of the domain. properties: type: extends: type @@ -31,7 +31,7 @@ $defs: type: array ordered: false description: >- - A non-exhaustive list of VRS variation contexts that satisfy the constraints of + A non-exhaustive list of VRS variation Constraints that satisfy the constraints of this categorical variant. items: oneOf: @@ -56,22 +56,21 @@ $defs: # ============================================================================= Constraint: - maturity: draft + maturity: trial use description: >- Constraints are used to construct an intensional semantics of categorical variant types. oneOf: - - $ref: "#/$defs/DefiningAlleleContext" - - $ref: "#/$defs/DefiningLocationContext" - - $ref: "#/$defs/CopyCountConstraint" - - $ref: "#/$defs/CopyChangeConstraint" + - $ref: "#/$defs/DefiningAlleleConstraint" + - $ref: "#/$defs/DefiningLocationConstraint" + - $ref: "#/$defs/CopyConstraint" heritableProperties: type: type: string heritableRequired: - type - DefiningAlleleContext: - maturity: draft + DefiningAlleleConstraint: + maturity: trial use type: object inherits: Constraint description: >- @@ -80,9 +79,9 @@ $defs: properties: type: extends: type - const: DefiningAlleleContext - default: DefiningAlleleContext - description: 'MUST be "DefiningAlleleContext"' + const: DefiningAlleleConstraint + default: DefiningAlleleConstraint + description: 'MUST be "DefiningAlleleConstraint"' allele: oneOf: - $ref: /ga4gh/schema/vrs/2.x/json/Allele @@ -100,7 +99,7 @@ $defs: - translates_to - translates_through description: >- - Defined relationships from which members relate to the defining context. + Defined relationships from which members relate to the defining allele. ``sequence_liftover`` refers to variants or locations that represent a congruent concept on a differing assembly of a human genome (e.g. "GRCh37" and "GRCh38") or gene (e.g. Locus Reference Genomic) sequence. ``transcript_projection`` refers to variants or locations that occur on transcripts projected from the defined genomic concept. ``codon_translation`` @@ -108,8 +107,8 @@ $defs: required: - allele - DefiningLocationContext: - maturity: draft + DefiningLocationConstraint: + maturity: trial use type: object inherits: Constraint description: >- @@ -118,9 +117,9 @@ $defs: properties: type: extends: type - const: DefiningLocationContext - default: DefiningLocationContext - description: 'MUST be "DefiningLocationContext"' + const: DefiningLocationConstraint + default: DefiningLocationConstraint + description: 'MUST be "DefiningLocationConstraint"' location: oneOf: - $ref: /ga4gh/schema/vrs/2.x/json/SequenceLocation @@ -138,7 +137,7 @@ $defs: - translates_to - translates_through description: >- - Defined relationships from which members relate to the defining context. + Defined relationships from which members relate to the defining location. ``sequence_liftover`` refers to variants or locations that represent a congruent concept on a differing assembly of a human genome (e.g. "GRCh37" and "GRCh38") or gene (e.g. Locus Reference Genomic) sequence. ``transcript_projection`` refers to variants or locations that occur on transcripts projected from the defined genomic concept. ``codon_translation`` @@ -156,50 +155,37 @@ $defs: - location - matchCharacteristic - CopyCountConstraint: - maturity: draft + CopyConstraint: + maturity: trial use inherits: Constraint type: object description: - The absolute number of copies in a system + The quantity of copies or the type of copy change that a member of this + categorical variant must have. One and only one MUST be specified. properties: type: extends: type - const: CopyCountConstraint - default: CopyCountConstraint - description: 'MUST be "CopyCountConstraint"' + const: CopyConstraint + default: CopyConstraint + description: 'MUST be "CopyConstraint"' copies: + description: >- + The precise value or range of copies a member of this categorical + variant must have. oneOf: - - type: integer - - $ref: /ga4gh/schema/vrs/2.x/json/Range - required: - - copies - - CopyChangeConstraint: - maturity: draft - inherits: Constraint - type: object - description: - A representation of copy number change - properties: - type: - extends: type - const: CopyChangeConstraint - default: CopyChangeConstraint - description: 'MUST be "CopyChangeConstraint"' + - type: integer + - $ref: /ga4gh/schema/vrs/2.x/json/Range copyChange: - $ref: /ga4gh/schema/gks-core/1.x/json/Coding - items: - properties: - code: - enum: - - EFO:0030069 - - EFO:0020073 - - EFO:0030068 - - EFO:0030067 - - EFO:0030064 - - EFO:0030070 - - EFO:0030071 - - EFO:0030072 - required: - - copyChange \ No newline at end of file + description: >- + The type of copy change a member of this categorical variant must + have. + type: string + enum: + - EFO:0030069 + - EFO:0020073 + - EFO:0030068 + - EFO:0030067 + - EFO:0030064 + - EFO:0030070 + - EFO:0030071 + - EFO:0030072 \ No newline at end of file diff --git a/schema/cat-vrs/def/CategoricalVariant.rst b/schema/cat-vrs/def/CategoricalVariant.rst index dc9252d..eeea199 100644 --- a/schema/cat-vrs/def/CategoricalVariant.rst +++ b/schema/cat-vrs/def/CategoricalVariant.rst @@ -1,12 +1,11 @@ -.. 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`. +.. 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** -A representation of a categorically-defined domain for variation, in which individual contextual variation instances may be members of the domain. +A representation of a categorically-defined domain for variation, in which individual Constraintual variation instances may be members of the domain. **Information Model** @@ -49,7 +48,7 @@ Some CategoricalVariant attributes are inherited from :ref:`gks-core:Entity`. * - members - :ref:`Variation` | :ref:`IRI` - 0..m - - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant. + - A non-exhaustive list of VRS variation Constraints that satisfy the constraints of this categorical variant. * - constraints - :ref:`Constraint` - 0..m diff --git a/schema/cat-vrs/def/Constraint.rst b/schema/cat-vrs/def/Constraint.rst index b3d3bb8..f332d1d 100644 --- a/schema/cat-vrs/def/Constraint.rst +++ b/schema/cat-vrs/def/Constraint.rst @@ -1,7 +1,6 @@ -.. 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`. +.. 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** diff --git a/schema/cat-vrs/def/CopyChangeConstraint.rst b/schema/cat-vrs/def/CopyChangeConstraint.rst deleted file mode 100644 index fc22e11..0000000 --- a/schema/cat-vrs/def/CopyChangeConstraint.rst +++ /dev/null @@ -1,32 +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 representation of copy number change - -**Information Model** - -Some CopyChangeConstraint attributes are inherited from :ref:`Constraint`. - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Type - - Limits - - Description - * - type - - string - - 1..1 - - MUST be "CopyChangeConstraint" - * - copyChange - - :ref:`Coding` - - 1..1 - - diff --git a/schema/cat-vrs/def/CopyConstraint.rst b/schema/cat-vrs/def/CopyConstraint.rst new file mode 100644 index 0000000..ca73930 --- /dev/null +++ b/schema/cat-vrs/def/CopyConstraint.rst @@ -0,0 +1,35 @@ + +.. 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** + +The quantity of copies or the type of copy change that a member of this categorical variant must have. One and only one MUST be specified. + +**Information Model** + +Some CopyConstraint attributes are inherited from :ref:`Constraint`. + +.. list-table:: + :class: clean-wrap + :header-rows: 1 + :align: left + :widths: auto + + * - Field + - Type + - Limits + - Description + * - type + - string + - 1..1 + - MUST be "CopyConstraint" + * - copies + - integer | :ref:`Range` + - 0..1 + - The precise value or range of copies a member of this categorical variant must have. + * - copyChange + - string + - 0..1 + - The type of copy change a member of this categorical variant must have. diff --git a/schema/cat-vrs/def/CopyCountConstraint.rst b/schema/cat-vrs/def/CopyCountConstraint.rst deleted file mode 100644 index 1931447..0000000 --- a/schema/cat-vrs/def/CopyCountConstraint.rst +++ /dev/null @@ -1,32 +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** - -The absolute number of copies in a system - -**Information Model** - -Some CopyCountConstraint attributes are inherited from :ref:`Constraint`. - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Type - - Limits - - Description - * - type - - string - - 1..1 - - MUST be "CopyCountConstraint" - * - copies - - integer | :ref:`Range` - - 1..1 - - diff --git a/schema/cat-vrs/def/DefiningAlleleConstraint.rst b/schema/cat-vrs/def/DefiningAlleleConstraint.rst new file mode 100644 index 0000000..3d679a2 --- /dev/null +++ b/schema/cat-vrs/def/DefiningAlleleConstraint.rst @@ -0,0 +1,35 @@ + +.. 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** + +The defining allele and its associated relationships that are congruent with member variants. + +**Information Model** + +Some DefiningAlleleConstraint attributes are inherited from :ref:`Constraint`. + +.. list-table:: + :class: clean-wrap + :header-rows: 1 + :align: left + :widths: auto + + * - Field + - Type + - Limits + - Description + * - type + - string + - 1..1 + - MUST be "DefiningAlleleConstraint" + * - allele + - :ref:`Allele` | :ref:`IRI` + - 1..1 + - + * - relations + - string + - 0..m + - Defined relationships from which members relate to the defining allele. ``sequence_liftover`` refers to variants or locations that represent a congruent concept on a differing assembly of a human genome (e.g. "GRCh37" and "GRCh38") or gene (e.g. Locus Reference Genomic) sequence. ``transcript_projection`` refers to variants or locations that occur on transcripts projected from the defined genomic concept. ``codon_translation`` refers to variants or locations that translate from the codon(s) represented by the defined concept. diff --git a/schema/cat-vrs/def/DefiningAlleleContext.rst b/schema/cat-vrs/def/DefiningAlleleContext.rst deleted file mode 100644 index fb2ba55..0000000 --- a/schema/cat-vrs/def/DefiningAlleleContext.rst +++ /dev/null @@ -1,36 +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** - -The defining allele and its associated relationships that are congruent with member variants. - -**Information Model** - -Some DefiningAlleleContext attributes are inherited from :ref:`Constraint`. - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Type - - Limits - - Description - * - type - - string - - 1..1 - - MUST be "DefiningAlleleContext" - * - allele - - :ref:`Allele` | :ref:`IRI` - - 1..1 - - - * - relations - - string - - 0..m - - Defined relationships from which members relate to the defining context. ``sequence_liftover`` refers to variants or locations that represent a congruent concept on a differing assembly of a human genome (e.g. "GRCh37" and "GRCh38") or gene (e.g. Locus Reference Genomic) sequence. ``transcript_projection`` refers to variants or locations that occur on transcripts projected from the defined genomic concept. ``codon_translation`` refers to variants or locations that translate from the codon(s) represented by the defined concept. diff --git a/schema/cat-vrs/def/DefiningLocationConstraint.rst b/schema/cat-vrs/def/DefiningLocationConstraint.rst new file mode 100644 index 0000000..09bb033 --- /dev/null +++ b/schema/cat-vrs/def/DefiningLocationConstraint.rst @@ -0,0 +1,39 @@ + +.. 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** + +The defining location and its associated relationships that are congruent with member locations. + +**Information Model** + +Some DefiningLocationConstraint attributes are inherited from :ref:`Constraint`. + +.. list-table:: + :class: clean-wrap + :header-rows: 1 + :align: left + :widths: auto + + * - Field + - Type + - Limits + - Description + * - type + - string + - 1..1 + - MUST be "DefiningLocationConstraint" + * - location + - :ref:`SequenceLocation` | :ref:`IRI` + - 1..1 + - + * - relations + - string + - 0..m + - Defined relationships from which members relate to the defining location. ``sequence_liftover`` refers to variants or locations that represent a congruent concept on a differing assembly of a human genome (e.g. "GRCh37" and "GRCh38") or gene (e.g. Locus Reference Genomic) sequence. ``transcript_projection`` refers to variants or locations that occur on transcripts projected from the defined genomic concept. ``codon_translation`` refers to variants or locations that translate from the codon(s) represented by the defined concept. + * - matchCharacteristic + - string + - 1..1 + - A characteristic of the location that is used to match the defining location to member locations. diff --git a/schema/cat-vrs/def/DefiningLocationContext.rst b/schema/cat-vrs/def/DefiningLocationContext.rst deleted file mode 100644 index 0c68a77..0000000 --- a/schema/cat-vrs/def/DefiningLocationContext.rst +++ /dev/null @@ -1,40 +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** - -The defining location and its associated relationships that are congruent with member locations. - -**Information Model** - -Some DefiningLocationContext attributes are inherited from :ref:`Constraint`. - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Type - - Limits - - Description - * - type - - string - - 1..1 - - MUST be "DefiningLocationContext" - * - location - - :ref:`SequenceLocation` | :ref:`IRI` - - 1..1 - - - * - relations - - string - - 0..m - - Defined relationships from which members relate to the defining context. ``sequence_liftover`` refers to variants or locations that represent a congruent concept on a differing assembly of a human genome (e.g. "GRCh37" and "GRCh38") or gene (e.g. Locus Reference Genomic) sequence. ``transcript_projection`` refers to variants or locations that occur on transcripts projected from the defined genomic concept. ``codon_translation`` refers to variants or locations that translate from the codon(s) represented by the defined concept. - * - matchCharacteristic - - string - - 1..1 - - A characteristic of the location that is used to match the defining location to member locations. diff --git a/schema/cat-vrs/json/CanonicalAllele b/schema/cat-vrs/json/CanonicalAllele index 345b877..73406f0 100644 --- a/schema/cat-vrs/json/CanonicalAllele +++ b/schema/cat-vrs/json/CanonicalAllele @@ -15,7 +15,7 @@ "contains": { "allOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningAlleleContext" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningAlleleConstraint" }, { "type": "object", diff --git a/schema/cat-vrs/json/CategoricalCnv b/schema/cat-vrs/json/CategoricalCnv index 890decd..5f33c04 100644 --- a/schema/cat-vrs/json/CategoricalCnv +++ b/schema/cat-vrs/json/CategoricalCnv @@ -17,7 +17,7 @@ "contains": { "allOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningLocationContext" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningLocationConstraint" }, { "type": "object", @@ -36,10 +36,7 @@ "contains": { "anyOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyCountConstraint" - }, - { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyChangeConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyConstraint" } ] } diff --git a/schema/cat-vrs/json/CategoricalVariant b/schema/cat-vrs/json/CategoricalVariant index b8b27e1..000b13f 100644 --- a/schema/cat-vrs/json/CategoricalVariant +++ b/schema/cat-vrs/json/CategoricalVariant @@ -3,8 +3,8 @@ "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant", "title": "CategoricalVariant", "type": "object", - "maturity": "draft", - "description": "A representation of a categorically-defined domain for variation, in which individual contextual variation instances may be members of the domain.", + "maturity": "trial use", + "description": "A representation of a categorically-defined domain for variation, in which individual Constraintual variation instances may be members of the domain.", "properties": { "id": { "type": "string", @@ -46,7 +46,7 @@ "members": { "type": "array", "ordered": false, - "description": "A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.", + "description": "A non-exhaustive list of VRS variation Constraints that satisfy the constraints of this categorical variant.", "items": { "oneOf": [ { @@ -64,16 +64,13 @@ "items": { "oneOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyChangeConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyConstraint" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyCountConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningAlleleConstraint" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningAlleleContext" - }, - { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningLocationContext" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningLocationConstraint" } ] } diff --git a/schema/cat-vrs/json/Constraint b/schema/cat-vrs/json/Constraint index 21d49c5..1f26019 100644 --- a/schema/cat-vrs/json/Constraint +++ b/schema/cat-vrs/json/Constraint @@ -3,20 +3,17 @@ "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/Constraint", "title": "Constraint", "type": "object", - "maturity": "draft", + "maturity": "trial use", "description": "Constraints are used to construct an intensional semantics of categorical variant types.", "oneOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyChangeConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyConstraint" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyCountConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningAlleleConstraint" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningAlleleContext" - }, - { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningLocationContext" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningLocationConstraint" } ] } \ No newline at end of file diff --git a/schema/cat-vrs/json/CopyChangeConstraint b/schema/cat-vrs/json/CopyChangeConstraint deleted file mode 100644 index 6de3d40..0000000 --- a/schema/cat-vrs/json/CopyChangeConstraint +++ /dev/null @@ -1,40 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/CopyChangeConstraint", - "title": "CopyChangeConstraint", - "type": "object", - "maturity": "draft", - "description": "A representation of copy number change", - "properties": { - "type": { - "type": "string", - "const": "CopyChangeConstraint", - "default": "CopyChangeConstraint", - "description": "MUST be \"CopyChangeConstraint\"" - }, - "copyChange": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Coding", - "items": { - "properties": { - "code": { - "enum": [ - "EFO:0030069", - "EFO:0020073", - "EFO:0030068", - "EFO:0030067", - "EFO:0030064", - "EFO:0030070", - "EFO:0030071", - "EFO:0030072" - ] - } - } - } - } - }, - "required": [ - "copyChange", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/cat-vrs/json/CopyConstraint b/schema/cat-vrs/json/CopyConstraint new file mode 100644 index 0000000..6de3398 --- /dev/null +++ b/schema/cat-vrs/json/CopyConstraint @@ -0,0 +1,45 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/CopyConstraint", + "title": "CopyConstraint", + "type": "object", + "maturity": "trial use", + "description": "The quantity of copies or the type of copy change that a member of this categorical variant must have. One and only one MUST be specified.", + "properties": { + "type": { + "type": "string", + "const": "CopyConstraint", + "default": "CopyConstraint", + "description": "MUST be \"CopyConstraint\"" + }, + "copies": { + "description": "The precise value or range of copies a member of this categorical variant must have.", + "oneOf": [ + { + "$ref": "/ga4gh/schema/vrs/2.x/json/Range" + }, + { + "type": "integer" + } + ] + }, + "copyChange": { + "description": "The type of copy change a member of this categorical variant must have.", + "type": "string", + "enum": [ + "EFO:0030069", + "EFO:0020073", + "EFO:0030068", + "EFO:0030067", + "EFO:0030064", + "EFO:0030070", + "EFO:0030071", + "EFO:0030072" + ] + } + }, + "required": [ + "type" + ], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/cat-vrs/json/CopyCountConstraint b/schema/cat-vrs/json/CopyCountConstraint deleted file mode 100644 index e1bcb69..0000000 --- a/schema/cat-vrs/json/CopyCountConstraint +++ /dev/null @@ -1,31 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/CopyCountConstraint", - "title": "CopyCountConstraint", - "type": "object", - "maturity": "draft", - "description": "The absolute number of copies in a system", - "properties": { - "type": { - "type": "string", - "const": "CopyCountConstraint", - "default": "CopyCountConstraint", - "description": "MUST be \"CopyCountConstraint\"" - }, - "copies": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Range" - }, - { - "type": "integer" - } - ] - } - }, - "required": [ - "copies", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/cat-vrs/json/DefiningAlleleContext b/schema/cat-vrs/json/DefiningAlleleConstraint similarity index 60% rename from schema/cat-vrs/json/DefiningAlleleContext rename to schema/cat-vrs/json/DefiningAlleleConstraint index c894d40..ce5c344 100644 --- a/schema/cat-vrs/json/DefiningAlleleContext +++ b/schema/cat-vrs/json/DefiningAlleleConstraint @@ -1,16 +1,16 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/DefiningAlleleContext", - "title": "DefiningAlleleContext", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/DefiningAlleleConstraint", + "title": "DefiningAlleleConstraint", "type": "object", - "maturity": "draft", + "maturity": "trial use", "description": "The defining allele and its associated relationships that are congruent with member variants.", "properties": { "type": { "type": "string", - "const": "DefiningAlleleContext", - "default": "DefiningAlleleContext", - "description": "MUST be \"DefiningAlleleContext\"" + "const": "DefiningAlleleConstraint", + "default": "DefiningAlleleConstraint", + "description": "MUST be \"DefiningAlleleConstraint\"" }, "allele": { "oneOf": [ @@ -36,7 +36,7 @@ "translates_through" ] }, - "description": "Defined relationships from which members relate to the defining context. ``sequence_liftover`` refers to variants or locations that represent a congruent concept on a differing assembly of a human genome (e.g. \"GRCh37\" and \"GRCh38\") or gene (e.g. Locus Reference Genomic) sequence. ``transcript_projection`` refers to variants or locations that occur on transcripts projected from the defined genomic concept. ``codon_translation`` refers to variants or locations that translate from the codon(s) represented by the defined concept." + "description": "Defined relationships from which members relate to the defining allele. ``sequence_liftover`` refers to variants or locations that represent a congruent concept on a differing assembly of a human genome (e.g. \"GRCh37\" and \"GRCh38\") or gene (e.g. Locus Reference Genomic) sequence. ``transcript_projection`` refers to variants or locations that occur on transcripts projected from the defined genomic concept. ``codon_translation`` refers to variants or locations that translate from the codon(s) represented by the defined concept." } }, "required": [ diff --git a/schema/cat-vrs/json/DefiningLocationContext b/schema/cat-vrs/json/DefiningLocationConstraint similarity index 66% rename from schema/cat-vrs/json/DefiningLocationContext rename to schema/cat-vrs/json/DefiningLocationConstraint index 45e2c3e..fb3fa8a 100644 --- a/schema/cat-vrs/json/DefiningLocationContext +++ b/schema/cat-vrs/json/DefiningLocationConstraint @@ -1,16 +1,16 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/DefiningLocationContext", - "title": "DefiningLocationContext", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/DefiningLocationConstraint", + "title": "DefiningLocationConstraint", "type": "object", - "maturity": "draft", + "maturity": "trial use", "description": "The defining location and its associated relationships that are congruent with member locations.", "properties": { "type": { "type": "string", - "const": "DefiningLocationContext", - "default": "DefiningLocationContext", - "description": "MUST be \"DefiningLocationContext\"" + "const": "DefiningLocationConstraint", + "default": "DefiningLocationConstraint", + "description": "MUST be \"DefiningLocationConstraint\"" }, "location": { "oneOf": [ @@ -36,7 +36,7 @@ "translates_through" ] }, - "description": "Defined relationships from which members relate to the defining context. ``sequence_liftover`` refers to variants or locations that represent a congruent concept on a differing assembly of a human genome (e.g. \"GRCh37\" and \"GRCh38\") or gene (e.g. Locus Reference Genomic) sequence. ``transcript_projection`` refers to variants or locations that occur on transcripts projected from the defined genomic concept. ``codon_translation`` refers to variants or locations that translate from the codon(s) represented by the defined concept." + "description": "Defined relationships from which members relate to the defining location. ``sequence_liftover`` refers to variants or locations that represent a congruent concept on a differing assembly of a human genome (e.g. \"GRCh37\" and \"GRCh38\") or gene (e.g. Locus Reference Genomic) sequence. ``transcript_projection`` refers to variants or locations that occur on transcripts projected from the defined genomic concept. ``codon_translation`` refers to variants or locations that translate from the codon(s) represented by the defined concept." }, "matchCharacteristic": { "type": "string", diff --git a/schema/cat-vrs/json/ProteinSequenceConsequence b/schema/cat-vrs/json/ProteinSequenceConsequence index de89a74..cfd6ce1 100644 --- a/schema/cat-vrs/json/ProteinSequenceConsequence +++ b/schema/cat-vrs/json/ProteinSequenceConsequence @@ -14,7 +14,7 @@ "contains": { "allOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningAlleleContext" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningAlleleConstraint" }, { "type": "object", diff --git a/schema/cat-vrs/recipes-source.yaml b/schema/cat-vrs/recipes-source.yaml index ecb3224..fc9bea0 100644 --- a/schema/cat-vrs/recipes-source.yaml +++ b/schema/cat-vrs/recipes-source.yaml @@ -22,7 +22,7 @@ $defs: constraints: contains: allOf: - - $ref: "/ga4gh/schema/cat-vrs/1.x/json/DefiningAlleleContext" + - $ref: "/ga4gh/schema/cat-vrs/1.x/json/DefiningAlleleConstraint" - type: object properties: relations: @@ -46,7 +46,7 @@ $defs: constraints: contains: allOf: - - $ref: "/ga4gh/schema/cat-vrs/1.x/json/DefiningAlleleContext" + - $ref: "/ga4gh/schema/cat-vrs/1.x/json/DefiningAlleleConstraint" - type: object properties: relations: @@ -68,7 +68,7 @@ $defs: allOf: - contains: allOf: - - $ref: "/ga4gh/schema/cat-vrs/1.x/json/DefiningLocationContext" + - $ref: "/ga4gh/schema/cat-vrs/1.x/json/DefiningLocationConstraint" - type: object properties: relations: @@ -76,5 +76,4 @@ $defs: const: liftover_to - contains: anyOf: - - $ref: "/ga4gh/schema/cat-vrs/1.x/json/CopyCountConstraint" - - $ref: "/ga4gh/schema/cat-vrs/1.x/json/CopyChangeConstraint" \ No newline at end of file + - $ref: "/ga4gh/schema/cat-vrs/1.x/json/CopyConstraint" \ No newline at end of file