diff --git a/examples/mappable-concept-gene.yaml b/examples/mappable-concept-gene.yaml index ca17471..89eaf0d 100644 --- a/examples/mappable-concept-gene.yaml +++ b/examples/mappable-concept-gene.yaml @@ -1,6 +1,6 @@ id: HGNC:1101 primaryCode: BRCA2 -label: BRCA2 DNA repair associated +name: BRCA2 DNA repair associated conceptType: Gene mappings: - coding: diff --git a/examples/simple-coding.yaml b/examples/simple-coding.yaml index d82f39d..576d44d 100644 --- a/examples/simple-coding.yaml +++ b/examples/simple-coding.yaml @@ -1,4 +1,4 @@ -label: foo +name: foo system: https://bar.com systemVersion: "2" code: "SCV213.1" diff --git a/schema/gks-core/def/Coding.rst b/schema/gks-core/def/Coding.rst index b40425a..973619a 100644 --- a/schema/gks-core/def/Coding.rst +++ b/schema/gks-core/def/Coding.rst @@ -1,5 +1,5 @@ -.. note:: This data class is at a **trial use** maturity level and may \ - change in future releases. Maturity \ +.. 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** @@ -34,7 +34,7 @@ Some Coding attributes are inherited from :ref:`Element`. - :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. - * - label + * - name - - string - 0..1 diff --git a/schema/gks-core/def/ConceptMapping.rst b/schema/gks-core/def/ConceptMapping.rst index badcae9..bcd33e4 100644 --- a/schema/gks-core/def/ConceptMapping.rst +++ b/schema/gks-core/def/ConceptMapping.rst @@ -1,5 +1,5 @@ -.. note:: This data class is at a **trial use** maturity level and may \ - change in future releases. Maturity \ +.. 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** diff --git a/schema/gks-core/def/Entity.rst b/schema/gks-core/def/Entity.rst index e7b7439..7b96191 100644 --- a/schema/gks-core/def/Entity.rst +++ b/schema/gks-core/def/Entity.rst @@ -30,7 +30,7 @@ Anything that exists, has existed, or will exist. - string - 1..1 - The name of the class that is instantiated by a data object representing the Entity. - * - label + * - name - - string - 0..1 @@ -40,7 +40,7 @@ Anything that exists, has existed, or will exist. - string - 0..1 - A free-text description of the Entity. - * - alternativeLabels + * - aliases - .. raw:: html diff --git a/schema/gks-core/def/MappableConcept.rst b/schema/gks-core/def/MappableConcept.rst index 24dbd98..f756262 100644 --- a/schema/gks-core/def/MappableConcept.rst +++ b/schema/gks-core/def/MappableConcept.rst @@ -1,10 +1,10 @@ -.. note:: This data class is at a **trial use** maturity level and may \ - change in future releases. Maturity \ +.. 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 concept label that may be mapped to one or more :ref:`Codings `. +A concept name that may be mapped to one or more :ref:`Codings `. **Information Model** @@ -39,7 +39,7 @@ Some MappableConcept attributes are inherited from :ref:`Element`. - string - 0..1 - A term indicating the type of concept being represented by the MappableConcept. - * - label + * - name - - string - 0..1 diff --git a/schema/gks-core/gks-core-source.yaml b/schema/gks-core/gks-core-source.yaml index 7478ac0..a6537ac 100644 --- a/schema/gks-core/gks-core-source.yaml +++ b/schema/gks-core/gks-core-source.yaml @@ -10,7 +10,7 @@ $defs: description: Anything that exists, has existed, or will exist. $comment: >- Entity is the root class of the 'gks-core' information model. All core classes that - have ids and other general metadata like label, description, type, or extensions descend from + have ids and other general metadata like name, description, type, or extensions descend from this class and inherit its attributes. heritableProperties: id: @@ -30,14 +30,14 @@ $defs: type: string description: >- The name of the class that is instantiated by a data object representing the Entity. - $comment: MUST be the label of a concrete class from the data model. - label: + $comment: MUST be the name of a concrete class from the data model. + name: type: string description: A primary name for the entity. description: type: string description: A free-text description of the Entity. - alternativeLabels: + aliases: type: array ordered: false items: @@ -116,12 +116,12 @@ $defs: MappableConcept: inherits: Element type: object - maturity: trial use + maturity: draft ga4gh: inherent: - primaryCode description: >- - A concept label that may be mapped to one or more :ref:`Codings `. + A concept name that may be mapped to one or more :ref:`Codings `. properties: conceptType: type: string @@ -131,7 +131,7 @@ $defs: This attribute can be used to indicate the type of concept being represented by the MappableConcept. For example, in a variant pathogenicity assessment, the conceptType could be 'Pathogenicity Strength', 'Disease', 'Phenotype', 'Drug', 'Tumor Type', 'Evidence Direction', 'Evidence Strength', etc. - label: + name: type: string description: A primary name for the concept. primaryCode: @@ -152,14 +152,14 @@ $defs: include a coding and a relation. anyOf: - required: - - label + - name - required: - primaryCode ConceptMapping: type: object inherits: Element - maturity: trial use + maturity: draft description: >- A mapping to a concept in a terminology or code system. properties: @@ -184,11 +184,11 @@ $defs: Coding: inherits: Element type: object - maturity: trial use + maturity: draft description: >- A structured representation of a code for a defined concept in a terminology or code system. properties: - label: + name: type: string description: The human-readable name for the coded concept, as defined by the code system. system: diff --git a/schema/gks-core/json/Coding b/schema/gks-core/json/Coding index 02738f4..dc85b41 100644 --- a/schema/gks-core/json/Coding +++ b/schema/gks-core/json/Coding @@ -3,7 +3,7 @@ "$id": "https://w3id.org/ga4gh/schema/gks-core/1.x/json/Coding", "title": "Coding", "type": "object", - "maturity": "trial use", + "maturity": "draft", "description": "A structured representation of a code for a defined concept in a terminology or code system.", "properties": { "id": { @@ -19,7 +19,7 @@ "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." }, - "label": { + "name": { "type": "string", "description": "The human-readable name for the coded concept, as defined by the code system." }, diff --git a/schema/gks-core/json/ConceptMapping b/schema/gks-core/json/ConceptMapping index 2b96def..b03ac19 100644 --- a/schema/gks-core/json/ConceptMapping +++ b/schema/gks-core/json/ConceptMapping @@ -3,7 +3,7 @@ "$id": "https://w3id.org/ga4gh/schema/gks-core/1.x/json/ConceptMapping", "title": "ConceptMapping", "type": "object", - "maturity": "trial use", + "maturity": "draft", "description": "A mapping to a concept in a terminology or code system.", "properties": { "id": { diff --git a/schema/gks-core/json/MappableConcept b/schema/gks-core/json/MappableConcept index d1dc5a4..9866c90 100644 --- a/schema/gks-core/json/MappableConcept +++ b/schema/gks-core/json/MappableConcept @@ -3,13 +3,13 @@ "$id": "https://w3id.org/ga4gh/schema/gks-core/1.x/json/MappableConcept", "title": "MappableConcept", "type": "object", - "maturity": "trial use", + "maturity": "draft", "ga4gh": { "inherent": [ "primaryCode" ] }, - "description": "A concept label that may be mapped to one or more Codings.", + "description": "A concept name that may be mapped to one or more Codings.", "properties": { "id": { "type": "string", @@ -29,7 +29,7 @@ "description": "A term indicating the type of concept being represented by the MappableConcept.", "$comment": "This attribute can be used to indicate the type of concept being represented by the MappableConcept. For example, in a variant pathogenicity assessment, the conceptType could be 'Pathogenicity Strength', 'Disease', 'Phenotype', 'Drug', 'Tumor Type', 'Evidence Direction', 'Evidence Strength', etc." }, - "label": { + "name": { "type": "string", "description": "A primary name for the concept." }, @@ -49,7 +49,7 @@ "anyOf": [ { "required": [ - "label" + "name" ] }, {