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

Inheritance

NamedThing
- OntologyClass
  - FunctionalAnnotationTerm
    - Pathway
    - OrthologyGroup

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

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

from schema: https://w3id.org/nmdc/nmdc

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:
  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: FunctionalAnnotationTerm
    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: FunctionalAnnotationTerm
    domain_of:
    - OntologyClass
    range: string
  relations:
    name: relations
    from_schema: https://w3id.org/nmdc/basic_classes
    rank: 1000
    alias: relations
    owner: FunctionalAnnotationTerm
    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: 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
    - PeptideQuantification
    - ProteinQuantification
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - OntologyRelation
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    range: uriorcurie
    required: true
class_uri: nmdc:FunctionalAnnotationTerm