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Class: OrthologyGroup

A set of genes or gene products in which all members are orthologous

URI: nmdc:OrthologyGroup

classDiagram class OrthologyGroup FunctionalAnnotationTerm <|-- OrthologyGroup OrthologyGroup : alternative_identifiers OrthologyGroup : description OrthologyGroup : id OrthologyGroup : name

Inheritance

Slots

Name Cardinality and Range Description Inheritance
id 1..1
Uriorcurie
A unique identifier for a thing NamedThing
name 0..1
String
A human readable label for an entity NamedThing
description 0..1
String
a human-readable description of a thing NamedThing
alternative_identifiers 0..*
Uriorcurie
A list of alternative identifiers for the entity NamedThing

Identifier and Mapping Information

Valid ID Prefixes

Instances of this class should have identifiers with one of the following prefixes:

  • CATH

  • EGGNOG

  • KEGG.ORTHOLOGY

  • PANTHER.FAMILY

  • PFAM

  • SUPFAM

  • TIGRFAM

Schema Source

Mappings

Mapping Type Mapped Value
self nmdc:OrthologyGroup
native nmdc:OrthologyGroup
exact biolink:GeneFamily

LinkML Source

Direct

name: OrthologyGroup
id_prefixes:
- CATH
- EGGNOG
- KEGG.ORTHOLOGY
- PANTHER.FAMILY
- PFAM
- SUPFAM
- TIGRFAM
description: A set of genes or gene products in which all members are orthologous
notes:
- KEGG.ORTHOLOGY prefix is used for KO numbers
from_schema: https://w3id.org/nmdc/nmdc
exact_mappings:
- biolink:GeneFamily
is_a: FunctionalAnnotationTerm

Induced

name: OrthologyGroup
id_prefixes:
- CATH
- EGGNOG
- KEGG.ORTHOLOGY
- PANTHER.FAMILY
- PFAM
- SUPFAM
- TIGRFAM
description: A set of genes or gene products in which all members are orthologous
notes:
- KEGG.ORTHOLOGY prefix is used for KO numbers
from_schema: https://w3id.org/nmdc/nmdc
exact_mappings:
- biolink:GeneFamily
is_a: FunctionalAnnotationTerm
attributes:
  id:
    name: id
    description: A unique identifier for a thing. Must be either a CURIE shorthand
      for a URI or a complete URI
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    identifier: true
    alias: id
    owner: OrthologyGroup
    domain_of:
    - Biosample
    - Study
    - NamedThing
    - Activity
    range: uriorcurie
    required: true
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
  name:
    name: name
    description: A human readable label for an entity
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: name
    owner: OrthologyGroup
    domain_of:
    - Protocol
    - NamedThing
    - PersonValue
    - Activity
    range: string
  description:
    name: description
    description: a human-readable description of a thing
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: dcterms:description
    alias: description
    owner: OrthologyGroup
    domain_of:
    - Study
    - NamedThing
    - ImageValue
    range: string
  alternative_identifiers:
    name: alternative_identifiers
    description: A list of alternative identifiers for the entity.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    multivalued: true
    alias: alternative_identifiers
    owner: OrthologyGroup
    domain_of:
    - Biosample
    - Study
    - NamedThing
    - MetaboliteQuantification
    range: uriorcurie
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$