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Class: FunctionalAnnotationTerm

Abstract grouping class for any term/descriptor that can be applied to a functional unit of a genome (protein, ncRNA, complex).

Note

This is an abstract class and should not be instantiated directly.

URI: nmdc:FunctionalAnnotationTerm

classDiagram class FunctionalAnnotationTerm click FunctionalAnnotationTerm href "../FunctionalAnnotationTerm" OntologyClass <|-- FunctionalAnnotationTerm click OntologyClass href "../OntologyClass" FunctionalAnnotationTerm <|-- Pathway click Pathway href "../Pathway" FunctionalAnnotationTerm <|-- OrthologyGroup click OrthologyGroup href "../OrthologyGroup" FunctionalAnnotationTerm : alternative_identifiers FunctionalAnnotationTerm : description FunctionalAnnotationTerm : id FunctionalAnnotationTerm : name FunctionalAnnotationTerm : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
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

Aliases

  • function
  • FunctionalAnnotation

TODOs

  • decide if this should be used for product naming (Duncan, 2021-04-02)
  • Retaining this even after removing Reaction. See todos on the Pathway and OrthologyGroup subclasses.

Identifier and Mapping Information

Schema Source

Mappings

Mapping Type Mapped Value
self nmdc:FunctionalAnnotationTerm
native nmdc:FunctionalAnnotationTerm

LinkML Source

Direct

name: FunctionalAnnotationTerm
description: Abstract grouping class for any term/descriptor that can be applied to
  a functional unit of a genome (protein, ncRNA, complex).
todos:
- decide if this should be used for product naming (Duncan, 2021-04-02)
- Retaining this even after removing Reaction. See todos on the Pathway and OrthologyGroup
  subclasses.
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- function
- FunctionalAnnotation
is_a: OntologyClass
abstract: true
class_uri: nmdc:FunctionalAnnotationTerm

Induced

name: FunctionalAnnotationTerm
description: Abstract grouping class for any term/descriptor that can be applied to
  a functional unit of a genome (protein, ncRNA, complex).
todos:
- decide if this should be used for product naming (Duncan, 2021-04-02)
- Retaining this even after removing Reaction. See todos on the Pathway and OrthologyGroup
  subclasses.
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- function
- FunctionalAnnotation
is_a: OntologyClass
abstract: true
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: FunctionalAnnotationTerm
    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: FunctionalAnnotationTerm
    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: FunctionalAnnotationTerm
    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: FunctionalAnnotationTerm
    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: FunctionalAnnotationTerm
    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:FunctionalAnnotationTerm