Skip to content

Class: GeneDescriptor

https://vrsatile.readthedocs.io/en/latest/value_object_descriptor/vod_index.html#gene-descriptor

URI: phenopackets:GeneDescriptor

erDiagram GeneDescriptor { stringList alternateIds stringList alternateSymbols string description string symbol string valueId stringList xrefs }

Slots

Name Cardinality and Range Description Inheritance
alternateIds 0..*
String		 Alternate IDs (should be CURIE) for the same concept may be placed in alterna... direct
alternateSymbols 0..*
String		 Takes the place of alternate_labels field in a generic descriptor direct
description 0..1
String		 A free-text description of the value object direct
symbol 0..1
String		 The primary gene symbol direct
valueId 0..1
String		 The official gene identifier as designated by the organism gene nomenclature ... direct
xrefs 0..*
String		 Related concept IDs (e direct

Usages

used by used in type used
VariationDescriptor geneContext range GeneDescriptor
GenomicInterpretation gene range GeneDescriptor

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/linkml/phenopackets/phenopackets

Mappings

Mapping Type Mapped Value
self phenopackets:GeneDescriptor
native phenopackets:GeneDescriptor

LinkML Source

Direct

name: GeneDescriptor
description: https://vrsatile.readthedocs.io/en/latest/value_object_descriptor/vod_index.html#gene-descriptor
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  alternateIds:
    name: alternateIds
    annotations:
      rank:
        tag: rank
        value: 4
    description: Alternate IDs (should be CURIE) for the same concept may be placed
      in alternate_ids
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    domain_of:
    - GeneDescriptor
    - Individual
    range: string
  alternateSymbols:
    name: alternateSymbols
    annotations:
      rank:
        tag: rank
        value: 5
    description: Takes the place of alternate_labels field in a generic descriptor
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    domain_of:
    - GeneDescriptor
    range: string
  description:
    name: description
    annotations:
      rank:
        tag: rank
        value: 3
    description: A free-text description of the value object
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    domain_of:
    - Cohort
    - ExternalReference
    - Measurement
    - PhenotypicFeature
    - Biosample
    - GeneDescriptor
    - VariationDescriptor
    range: string
  symbol:
    name: symbol
    annotations:
      rank:
        tag: rank
        value: 2
    description: The primary gene symbol. Takes the place of the label field in a
      generic descriptor
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - GeneDescriptor
    range: string
  valueId:
    name: valueId
    annotations:
      rank:
        tag: rank
        value: 1
    description: The official gene identifier as designated by the organism gene nomenclature
      committee e.g. HGNC:3477 or MGI:2385071 This should be a CURIE linking the reference
      to a namespace where it can be retrieved. Mirrors the value_id field of a generic
      value object descriptor
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - GeneDescriptor
    range: string
  xrefs:
    name: xrefs
    annotations:
      rank:
        tag: rank
        value: 6
    description: Related concept IDs (e.g. gene ortholog IDs) may be placed in xrefs
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    domain_of:
    - GeneDescriptor
    - VariationDescriptor
    range: string

Induced

name: GeneDescriptor
description: https://vrsatile.readthedocs.io/en/latest/value_object_descriptor/vod_index.html#gene-descriptor
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  alternateIds:
    name: alternateIds
    annotations:
      rank:
        tag: rank
        value: 4
    description: Alternate IDs (should be CURIE) for the same concept may be placed
      in alternate_ids
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    alias: alternateIds
    owner: GeneDescriptor
    domain_of:
    - GeneDescriptor
    - Individual
    range: string
  alternateSymbols:
    name: alternateSymbols
    annotations:
      rank:
        tag: rank
        value: 5
    description: Takes the place of alternate_labels field in a generic descriptor
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    alias: alternateSymbols
    owner: GeneDescriptor
    domain_of:
    - GeneDescriptor
    range: string
  description:
    name: description
    annotations:
      rank:
        tag: rank
        value: 3
    description: A free-text description of the value object
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    alias: description
    owner: GeneDescriptor
    domain_of:
    - Cohort
    - ExternalReference
    - Measurement
    - PhenotypicFeature
    - Biosample
    - GeneDescriptor
    - VariationDescriptor
    range: string
  symbol:
    name: symbol
    annotations:
      rank:
        tag: rank
        value: 2
    description: The primary gene symbol. Takes the place of the label field in a
      generic descriptor
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: symbol
    owner: GeneDescriptor
    domain_of:
    - GeneDescriptor
    range: string
  valueId:
    name: valueId
    annotations:
      rank:
        tag: rank
        value: 1
    description: The official gene identifier as designated by the organism gene nomenclature
      committee e.g. HGNC:3477 or MGI:2385071 This should be a CURIE linking the reference
      to a namespace where it can be retrieved. Mirrors the value_id field of a generic
      value object descriptor
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: valueId
    owner: GeneDescriptor
    domain_of:
    - GeneDescriptor
    range: string
  xrefs:
    name: xrefs
    annotations:
      rank:
        tag: rank
        value: 6
    description: Related concept IDs (e.g. gene ortholog IDs) may be placed in xrefs
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    alias: xrefs
    owner: GeneDescriptor
    domain_of:
    - GeneDescriptor
    - VariationDescriptor
    range: string