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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 click OrthologyGroup href "../OrthologyGroup" FunctionalAnnotationTerm <|-- OrthologyGroup click FunctionalAnnotationTerm href "../FunctionalAnnotationTerm" OrthologyGroup : alternative_identifiers OrthologyGroup : alternative_names OrthologyGroup : definition OrthologyGroup : description OrthologyGroup : id OrthologyGroup : name OrthologyGroup : relations OrthologyGroup --> "*" OntologyRelation : relations click OntologyRelation href "../OntologyRelation" OrthologyGroup : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
alternative_names *
String		 A list of alternative names used to refer to the entity OntologyClass
definition 0..1
String		 The definition of the ontology term as provided by the ontology OntologyClass
relations *
OntologyRelation		 OntologyClass
id 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 *
Uriorcurie		 A list of alternative identifiers for the entity NamedThing
type 1
Uriorcurie		 the class_uri of the class that has been instantiated NamedThing

TODOs

  • is OrthologyGroup instantiated in an MongoDB collection? Aren't Pathways searchable in the Data Portal?

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
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

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
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:
  alternative_names:
    name: alternative_names
    description: A list of alternative names used to refer to the entity. The distinction
      between name and alternative names is application-specific.
    from_schema: https://w3id.org/nmdc/nmdc
    exact_mappings:
    - dcterms:alternative
    - skos:altLabel
    rank: 1000
    alias: alternative_names
    owner: OrthologyGroup
    domain_of:
    - OntologyClass
    - Study
    range: string
    multivalued: true
  definition:
    name: definition
    description: The definition of the ontology term as provided by the ontology.
    from_schema: https://w3id.org/nmdc/basic_classes
    rank: 1000
    alias: definition
    owner: OrthologyGroup
    domain_of:
    - OntologyClass
    range: string
  relations:
    name: relations
    from_schema: https://w3id.org/nmdc/basic_classes
    rank: 1000
    alias: relations
    owner: OrthologyGroup
    domain_of:
    - OntologyClass
    range: OntologyRelation
    multivalued: true
    inlined: true
    inlined_as_list: true
  id:
    name: id
    description: A unique identifier for a thing. Must be either a CURIE shorthand
      for a URI or a complete URI
    notes:
    - The identifiers for terms from external ontologies can't have their ids constrained
      to the nmdc namespace
    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
    - PeptideQuantification
    - ProteinQuantification
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - OntologyRelation
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    range: uriorcurie
    required: true
class_uri: nmdc:OrthologyGroup