Class: OrthologyGroup

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
todos:
- is OrthologyGroup instantiated in an MongoDB collection? Aren't Pathways searchable
  in the Data Portal?
notes:
- KEGG.ORTHOLOGY prefix is used for KO numbers
from_schema: https://w3id.org/nmdc/nmdc
exact_mappings:
- biolink:GeneFamily
is_a: FunctionalAnnotationTerm
class_uri: nmdc:OrthologyGroup

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
todos:
- is OrthologyGroup instantiated in an MongoDB collection? Aren't Pathways searchable
  in the Data Portal?
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
    notes:
    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'
    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters
      will be accepted
    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked
      via per-class id slot usage assertions
    - minting authority shoulders should probably be enumerated and checked in the
      pattern
    examples:
    - value: nmdc:mgmag-00-x012.1_7_c1
      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    identifier: true
    alias: id
    owner: OrthologyGroup
    domain_of:
    - NamedThing
    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:
    - PersonValue
    - NamedThing
    - Protocol
    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:
    - ImageValue
    - NamedThing
    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
    alias: alternative_identifiers
    owner: OrthologyGroup
    domain_of:
    - MetaboliteIdentification
    - NamedThing
    range: uriorcurie
    multivalued: true
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
  type:
    name: type
    description: the class_uri of the class that has been instantiated
    notes:
    - replaces legacy nmdc:type slot
    - makes it easier to read example data files
    - required for polymorphic MongoDB collections
    examples:
    - value: nmdc:Biosample
    - value: nmdc:Study
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://github.com/microbiomedata/nmdc-schema/issues/1048
    - https://github.com/microbiomedata/nmdc-schema/issues/1233
    - https://github.com/microbiomedata/nmdc-schema/issues/248
    rank: 1000
    slot_uri: rdf:type
    designates_type: true
    alias: type
    owner: OrthologyGroup
    domain_of:
    - EukEval
    - FunctionalAnnotationAggMember
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    - PeptideQuantification
    - ProteinQuantification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    range: uriorcurie
    required: true
class_uri: nmdc:OrthologyGroup