From e6a29f7296d5e177ad973786a0440de9e3c85c6e Mon Sep 17 00:00:00 2001 From: Lawrence Babb Date: Wed, 4 Sep 2024 22:51:04 -0400 Subject: [PATCH] added connect label to schema id --- schema/cat-vrs/cat-vrs-source.yaml | 20 ++++++++-------- schema/cat-vrs/def/CanonicalAllele.rst | 10 ++++---- schema/cat-vrs/def/CategoricalCnv.rst | 14 +++++------ schema/cat-vrs/def/CategoricalVariation.rst | 10 ++++---- schema/cat-vrs/def/DescribedVariation.rst | 6 ++--- schema/cat-vrs/def/NumberChange.rst | 2 +- schema/cat-vrs/def/NumberCount.rst | 2 +- .../def/ProteinSequenceConsequence.rst | 10 ++++---- schema/cat-vrs/json/CanonicalAllele | 19 +++++++-------- schema/cat-vrs/json/CategoricalCnv | 23 ++++++++----------- schema/cat-vrs/json/CategoricalVariation | 10 ++++---- schema/cat-vrs/json/DescribedVariation | 15 +++++------- schema/cat-vrs/json/NumberChange | 4 ++-- schema/cat-vrs/json/NumberCount | 4 ++-- .../cat-vrs/json/ProteinSequenceConsequence | 19 +++++++-------- schema/cat-vrs/json/QuantityVariance | 2 +- 16 files changed, 79 insertions(+), 91 deletions(-) diff --git a/schema/cat-vrs/cat-vrs-source.yaml b/schema/cat-vrs/cat-vrs-source.yaml index 53dddd2..bc40678 100644 --- a/schema/cat-vrs/cat-vrs-source.yaml +++ b/schema/cat-vrs/cat-vrs-source.yaml @@ -1,5 +1,5 @@ $schema: "https://json-schema.org/draft/2020-12/schema" -$id: "https://w3id.org/ga4gh/schema/cat-vrs/1.x/cat-vrs-source.yaml" +$id: "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-connect.2024-09/cat-vrs-source.yaml" title: GA4GH-Cat-VRS-Definitions type: object strict: true @@ -37,7 +37,7 @@ $defs: this categorical variant. items: oneOf: - - $ref: "/ga4gh/schema/vrs/2.x/json/Variation" + - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Variation" - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" ProteinSequenceConsequence: @@ -58,7 +58,7 @@ $defs: description: 'MUST be "ProteinSequenceConsequence"' definingContext: oneOf: - - $ref: "/ga4gh/schema/vrs/2.x/json/Allele" + - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Allele" - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" description: >- The `VRS Allele `_ @@ -84,7 +84,7 @@ $defs: description: 'MUST be "CanonicalAllele"' definingContext: oneOf: - - $ref: "/ga4gh/schema/vrs/2.x/json/Allele" + - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Allele" - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" description: >- The `VRS Allele `_ @@ -111,10 +111,10 @@ $defs: description: 'MUST be "CategoricalCnv"' location: oneOf: - - $ref: "/ga4gh/schema/vrs/2.x/json/SequenceLocation" + - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/SequenceLocation" - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" description: >- - A `VRS Location `_ + A `VRS Location `_ object that represents a sequence derived from that location, and is congruent with locations on alternate reference sequences. locationMatchCharacteristic: @@ -138,7 +138,7 @@ $defs: copies: oneOf: - type: integer - - $ref: "/ga4gh/schema/vrs/2.x/json/Range" + - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Range" description: >- The integral number of copies of the subject in a system. required: @@ -239,7 +239,7 @@ $defs: count: oneOf: - type: integer - - $ref: "/ga4gh/schema/vrs/2.x/json/Range" + - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Range" description: >- The integral quantity or quantity range of the subject in a system required: [ "count" ] @@ -265,7 +265,7 @@ $defs: change: oneOf: - type: integer - - $ref: "/ga4gh/schema/vrs/2.x/json/Range" + - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Range" - copyChange: type: string enum: [ "EFO:0030069", "EFO:0020073", "EFO:0030068", "EFO:0030067", "EFO:0030064", "EFO:0030070", @@ -322,7 +322,7 @@ $defs: # copies: # oneOf: # - type: integer - # - $ref: "/ga4gh/schema/vrs/2.x/json/Range" + # - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Range" # description: >- # The integral number of copies of the subject in a system. # required: diff --git a/schema/cat-vrs/def/CanonicalAllele.rst b/schema/cat-vrs/def/CanonicalAllele.rst index 7c0f7ee..e7a8a41 100644 --- a/schema/cat-vrs/def/CanonicalAllele.rst +++ b/schema/cat-vrs/def/CanonicalAllele.rst @@ -19,7 +19,7 @@ Some CanonicalAllele attributes are inherited from :ref:`CategoricalVariation`. * - 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. + - 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 - string - 0..1 @@ -27,7 +27,7 @@ Some CanonicalAllele attributes are inherited from :ref:`CategoricalVariation`. * - description - string - 0..1 - - A free-text description of the Entity. + - A free-text description of the entity. * - alternativeLabels - string - 0..m @@ -35,13 +35,13 @@ Some CanonicalAllele attributes are inherited from :ref:`CategoricalVariation`. * - extensions - `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. + - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems. * - mappings - `ConceptMapping `_ - 0..m - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation. * - members - - `Variation `_ | `IRI `_ + - `Variation `_ | `IRI `_ - 0..m - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant. * - type @@ -49,6 +49,6 @@ Some CanonicalAllele attributes are inherited from :ref:`CategoricalVariation`. - 1..1 - MUST be "CanonicalAllele" * - definingContext - - `Allele `_ | `IRI `_ + - `Allele `_ | `IRI `_ - 1..1 - The `VRS Allele `_ object that is congruent with variants on alternate reference sequences. diff --git a/schema/cat-vrs/def/CategoricalCnv.rst b/schema/cat-vrs/def/CategoricalCnv.rst index 12105a5..d8bdbbb 100644 --- a/schema/cat-vrs/def/CategoricalCnv.rst +++ b/schema/cat-vrs/def/CategoricalCnv.rst @@ -19,7 +19,7 @@ Some CategoricalCnv attributes are inherited from :ref:`CategoricalVariation`. * - 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. + - 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 - string - 0..1 @@ -27,7 +27,7 @@ Some CategoricalCnv attributes are inherited from :ref:`CategoricalVariation`. * - description - string - 0..1 - - A free-text description of the Entity. + - A free-text description of the entity. * - alternativeLabels - string - 0..m @@ -35,13 +35,13 @@ Some CategoricalCnv attributes are inherited from :ref:`CategoricalVariation`. * - extensions - `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. + - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems. * - mappings - `ConceptMapping `_ - 0..m - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation. * - members - - `Variation `_ | `IRI `_ + - `Variation `_ | `IRI `_ - 0..m - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant. * - type @@ -49,9 +49,9 @@ Some CategoricalCnv attributes are inherited from :ref:`CategoricalVariation`. - 1..1 - MUST be "CategoricalCnv" * - location - - `SequenceLocation `_ | `IRI `_ + - `SequenceLocation `_ | `IRI `_ - 1..1 - - A `VRS Location `_ object that represents a sequence derived from that location, and is congruent with locations on alternate reference sequences. + - A `VRS Location `_ object that represents a sequence derived from that location, and is congruent with locations on alternate reference sequences. * - locationMatchCharacteristic - string - 0..1 @@ -61,6 +61,6 @@ Some CategoricalCnv attributes are inherited from :ref:`CategoricalVariation`. - 0..1 - 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 - - integer | `Range `_ + - integer | `Range `_ - 0..1 - The integral number of copies of the subject in a system. diff --git a/schema/cat-vrs/def/CategoricalVariation.rst b/schema/cat-vrs/def/CategoricalVariation.rst index 4202df5..c0cf7d9 100644 --- a/schema/cat-vrs/def/CategoricalVariation.rst +++ b/schema/cat-vrs/def/CategoricalVariation.rst @@ -19,11 +19,11 @@ Some CategoricalVariation attributes are inherited from :ref:`gks.core-im:Domain * - 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. + - 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). * - type - string - 1..1 - - The name of the class that is instantiated by a data object representing the Entity. + - * - label - string - 0..1 @@ -31,7 +31,7 @@ Some CategoricalVariation attributes are inherited from :ref:`gks.core-im:Domain * - description - string - 0..1 - - A free-text description of the Entity. + - A free-text description of the entity. * - alternativeLabels - string - 0..m @@ -39,12 +39,12 @@ Some CategoricalVariation attributes are inherited from :ref:`gks.core-im:Domain * - extensions - `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. + - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems. * - mappings - `ConceptMapping `_ - 0..m - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation. * - members - - `Variation `_ | `IRI `_ + - `Variation `_ | `IRI `_ - 0..m - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant. diff --git a/schema/cat-vrs/def/DescribedVariation.rst b/schema/cat-vrs/def/DescribedVariation.rst index b58362f..3543c02 100644 --- a/schema/cat-vrs/def/DescribedVariation.rst +++ b/schema/cat-vrs/def/DescribedVariation.rst @@ -19,7 +19,7 @@ Some DescribedVariation attributes are inherited from :ref:`CategoricalVariation * - 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. + - 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). * - alternativeLabels - string - 0..m @@ -27,13 +27,13 @@ Some DescribedVariation attributes are inherited from :ref:`CategoricalVariation * - extensions - `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. + - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems. * - mappings - `ConceptMapping `_ - 0..m - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation. * - members - - `Variation `_ | `IRI `_ + - `Variation `_ | `IRI `_ - 0..m - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant. * - type diff --git a/schema/cat-vrs/def/NumberChange.rst b/schema/cat-vrs/def/NumberChange.rst index b9e6197..0c041a7 100644 --- a/schema/cat-vrs/def/NumberChange.rst +++ b/schema/cat-vrs/def/NumberChange.rst @@ -20,6 +20,6 @@ A quantitative assessment of a unit within a system (e.g. genome, cell, etc.) re - 0..1 - MUST be "NumberChange" * - change - - integer | `Range `_ | string + - integer | `Range `_ | string - 0..1 - a quantitative or qualitative value of the measurement with respect to a baseline (0). If qualitative, 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). diff --git a/schema/cat-vrs/def/NumberCount.rst b/schema/cat-vrs/def/NumberCount.rst index f965bb9..fa443f5 100644 --- a/schema/cat-vrs/def/NumberCount.rst +++ b/schema/cat-vrs/def/NumberCount.rst @@ -20,6 +20,6 @@ The absolute count of a discrete assayable unit (e.g. chromosome, gene, or seque - 0..1 - MUST be "NumberCount" * - count - - integer | `Range `_ + - integer | `Range `_ - 1..1 - The integral quantity or quantity range of the subject in a system diff --git a/schema/cat-vrs/def/ProteinSequenceConsequence.rst b/schema/cat-vrs/def/ProteinSequenceConsequence.rst index 94d005b..d49e208 100644 --- a/schema/cat-vrs/def/ProteinSequenceConsequence.rst +++ b/schema/cat-vrs/def/ProteinSequenceConsequence.rst @@ -19,7 +19,7 @@ Some ProteinSequenceConsequence attributes are inherited from :ref:`CategoricalV * - 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. + - 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 - string - 0..1 @@ -27,7 +27,7 @@ Some ProteinSequenceConsequence attributes are inherited from :ref:`CategoricalV * - description - string - 0..1 - - A free-text description of the Entity. + - A free-text description of the entity. * - alternativeLabels - string - 0..m @@ -35,13 +35,13 @@ Some ProteinSequenceConsequence attributes are inherited from :ref:`CategoricalV * - extensions - `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. + - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems. * - mappings - `ConceptMapping `_ - 0..m - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation. * - members - - `Variation `_ | `IRI `_ + - `Variation `_ | `IRI `_ - 0..m - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant. * - type @@ -49,6 +49,6 @@ Some ProteinSequenceConsequence attributes are inherited from :ref:`CategoricalV - 1..1 - MUST be "ProteinSequenceConsequence" * - definingContext - - `Allele `_ | `IRI `_ + - `Allele `_ | `IRI `_ - 1..1 - The `VRS Allele `_ object that is congruent with (projects to the same codons) as alleles on other protein reference sequences. diff --git a/schema/cat-vrs/json/CanonicalAllele b/schema/cat-vrs/json/CanonicalAllele index 5601d33..83972e2 100644 --- a/schema/cat-vrs/json/CanonicalAllele +++ b/schema/cat-vrs/json/CanonicalAllele @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/CanonicalAllele", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-connect.2024-09/json/CanonicalAllele", "title": "CanonicalAllele", "type": "object", "maturity": "draft", @@ -8,8 +8,7 @@ "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, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", - "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." + "description": "The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE)." }, "label": { "type": "string", @@ -17,7 +16,7 @@ }, "description": { "type": "string", - "description": "A free-text description of the Entity." + "description": "A free-text description of the entity." }, "alternativeLabels": { "type": "array", @@ -33,8 +32,7 @@ "items": { "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension" }, - "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", - "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." + "description": "A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." }, "mappings": { "type": "array", @@ -54,17 +52,16 @@ "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" }, { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" + "$ref": "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Variation" } ] } }, "type": { "type": "string", - "description": "MUST be \"CanonicalAllele\"", - "$comment": "MUST be the label of a concrete class from the data model.", "const": "CanonicalAllele", - "default": "CanonicalAllele" + "default": "CanonicalAllele", + "description": "MUST be \"CanonicalAllele\"" }, "definingContext": { "oneOf": [ @@ -72,7 +69,7 @@ "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" }, { - "$ref": "/ga4gh/schema/vrs/2.x/json/Allele" + "$ref": "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Allele" } ], "description": "The [VRS Allele](https://vrs.ga4gh.org/en/2.0/terms_and_model.html#allele) object that is congruent with variants on alternate reference sequences." diff --git a/schema/cat-vrs/json/CategoricalCnv b/schema/cat-vrs/json/CategoricalCnv index 052f1f8..45329f6 100644 --- a/schema/cat-vrs/json/CategoricalCnv +++ b/schema/cat-vrs/json/CategoricalCnv @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/CategoricalCnv", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-connect.2024-09/json/CategoricalCnv", "title": "CategoricalCnv", "type": "object", "maturity": "draft", @@ -8,8 +8,7 @@ "properties": { "id": { "type": "string", - "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", - "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." + "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", @@ -17,7 +16,7 @@ }, "description": { "type": "string", - "description": "A free-text description of the Entity." + "description": "A free-text description of the entity." }, "alternativeLabels": { "type": "array", @@ -33,8 +32,7 @@ "items": { "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension" }, - "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", - "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." + "description": "A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." }, "mappings": { "type": "array", @@ -54,17 +52,16 @@ "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" }, { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" + "$ref": "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Variation" } ] } }, "type": { "type": "string", - "description": "MUST be \"CategoricalCnv\"", - "$comment": "MUST be the label of a concrete class from the data model.", "const": "CategoricalCnv", - "default": "CategoricalCnv" + "default": "CategoricalCnv", + "description": "MUST be \"CategoricalCnv\"" }, "location": { "oneOf": [ @@ -72,10 +69,10 @@ "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" }, { - "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation" + "$ref": "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/SequenceLocation" } ], - "description": "A [VRS Location](https://vrs.ga4gh.org/en/2.x/concepts/location/SequenceLocation.html) object that represents a sequence derived from that location, and is congruent with locations on alternate reference sequences." + "description": "A [VRS Location](https://vrs.ga4gh.org/en/2.0.0-ballot.2024-08.1/concepts/location/SequenceLocation.html) object that represents a sequence derived from that location, and is congruent with locations on alternate reference sequences." }, "locationMatchCharacteristic": { "type": "string", @@ -104,7 +101,7 @@ "copies": { "oneOf": [ { - "$ref": "/ga4gh/schema/vrs/2.x/json/Range" + "$ref": "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Range" }, { "type": "integer" diff --git a/schema/cat-vrs/json/CategoricalVariation b/schema/cat-vrs/json/CategoricalVariation index 06da9ed..3f70723 100644 --- a/schema/cat-vrs/json/CategoricalVariation +++ b/schema/cat-vrs/json/CategoricalVariation @@ -1,21 +1,21 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariation", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-connect.2024-09/json/CategoricalVariation", "title": "CategoricalVariation", "type": "object", "description": "A representation of a categorically-defined domain for variation, in which individual contextual variation instances may be members of the domain.", "oneOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CanonicalAllele" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-connect.2024-09/json/CanonicalAllele" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalCnv" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-connect.2024-09/json/CategoricalCnv" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DescribedVariation" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-connect.2024-09/json/DescribedVariation" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/ProteinSequenceConsequence" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-connect.2024-09/json/ProteinSequenceConsequence" } ] } \ No newline at end of file diff --git a/schema/cat-vrs/json/DescribedVariation b/schema/cat-vrs/json/DescribedVariation index dfacdba..72a5418 100644 --- a/schema/cat-vrs/json/DescribedVariation +++ b/schema/cat-vrs/json/DescribedVariation @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/DescribedVariation", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-connect.2024-09/json/DescribedVariation", "title": "DescribedVariation", "type": "object", "maturity": "draft", @@ -8,8 +8,7 @@ "properties": { "id": { "type": "string", - "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", - "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." + "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)." }, "alternativeLabels": { "type": "array", @@ -25,8 +24,7 @@ "items": { "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension" }, - "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", - "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." + "description": "A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." }, "mappings": { "type": "array", @@ -46,17 +44,16 @@ "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" }, { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" + "$ref": "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Variation" } ] } }, "type": { "type": "string", - "description": "MUST be \"DescribedVariation\"", - "$comment": "MUST be the label of a concrete class from the data model.", "const": "DescribedVariation", - "default": "DescribedVariation" + "default": "DescribedVariation", + "description": "MUST be \"DescribedVariation\"" }, "label": { "type": "string", diff --git a/schema/cat-vrs/json/NumberChange b/schema/cat-vrs/json/NumberChange index 6cd1885..b2706fa 100644 --- a/schema/cat-vrs/json/NumberChange +++ b/schema/cat-vrs/json/NumberChange @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/NumberChange", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-connect.2024-09/json/NumberChange", "title": "NumberChange", "type": "object", "maturity": "draft", @@ -15,7 +15,7 @@ "change": { "oneOf": [ { - "$ref": "/ga4gh/schema/vrs/2.x/json/Range" + "$ref": "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Range" }, { "type": "integer" diff --git a/schema/cat-vrs/json/NumberCount b/schema/cat-vrs/json/NumberCount index 7f402bd..d53f91b 100644 --- a/schema/cat-vrs/json/NumberCount +++ b/schema/cat-vrs/json/NumberCount @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/NumberCount", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-connect.2024-09/json/NumberCount", "title": "NumberCount", "type": "object", "maturity": "draft", @@ -15,7 +15,7 @@ "count": { "oneOf": [ { - "$ref": "/ga4gh/schema/vrs/2.x/json/Range" + "$ref": "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Range" }, { "type": "integer" diff --git a/schema/cat-vrs/json/ProteinSequenceConsequence b/schema/cat-vrs/json/ProteinSequenceConsequence index 9f599a2..19d8258 100644 --- a/schema/cat-vrs/json/ProteinSequenceConsequence +++ b/schema/cat-vrs/json/ProteinSequenceConsequence @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/ProteinSequenceConsequence", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-connect.2024-09/json/ProteinSequenceConsequence", "title": "ProteinSequenceConsequence", "type": "object", "maturity": "draft", @@ -8,8 +8,7 @@ "properties": { "id": { "type": "string", - "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", - "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." + "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", @@ -17,7 +16,7 @@ }, "description": { "type": "string", - "description": "A free-text description of the Entity." + "description": "A free-text description of the entity." }, "alternativeLabels": { "type": "array", @@ -33,8 +32,7 @@ "items": { "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension" }, - "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", - "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." + "description": "A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." }, "mappings": { "type": "array", @@ -54,17 +52,16 @@ "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" }, { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" + "$ref": "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Variation" } ] } }, "type": { "type": "string", - "description": "MUST be \"ProteinSequenceConsequence\"", - "$comment": "MUST be the label of a concrete class from the data model.", "const": "ProteinSequenceConsequence", - "default": "ProteinSequenceConsequence" + "default": "ProteinSequenceConsequence", + "description": "MUST be \"ProteinSequenceConsequence\"" }, "definingContext": { "oneOf": [ @@ -72,7 +69,7 @@ "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" }, { - "$ref": "/ga4gh/schema/vrs/2.x/json/Allele" + "$ref": "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Allele" } ], "description": "The [VRS Allele](https://vrs.ga4gh.org/en/2.0/terms_and_model.html#allele) object that is congruent with (projects to the same codons) as alleles on other protein reference sequences." diff --git a/schema/cat-vrs/json/QuantityVariance b/schema/cat-vrs/json/QuantityVariance index 9f4dc40..797f17e 100644 --- a/schema/cat-vrs/json/QuantityVariance +++ b/schema/cat-vrs/json/QuantityVariance @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/QuantityVariance", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-connect.2024-09/json/QuantityVariance", "title": "QuantityVariance", "type": "object", "maturity": "draft",