Class: ControlledIdentifiedTermValue

A controlled term or class from an ontology, requiring the presence of term with an id

classDiagram class ControlledIdentifiedTermValue click ControlledIdentifiedTermValue href "../ControlledIdentifiedTermValue" ControlledTermValue <|-- ControlledIdentifiedTermValue click ControlledTermValue href "../ControlledTermValue" ControlledIdentifiedTermValue : has_raw_value ControlledIdentifiedTermValue : term ControlledIdentifiedTermValue --> "1" OntologyClass : term click OntologyClass href "../OntologyClass" ControlledIdentifiedTermValue : type

Inheritance

AttributeValue
- ControlledTermValue
  - ControlledIdentifiedTermValue

Slots

Name	Cardinality and Range	Description	Inheritance
term	1 OntologyClass	pointer to an ontology class	ControlledTermValue
has_raw_value	0..1 String	The value that was specified for an annotation in raw form, i	AttributeValue
type	1 Uriorcurie	the class_uri of the class that has been instantiated	AttributeValue

Usages

used by	used in	type	used
Biosample	host_taxid	range	ControlledIdentifiedTermValue
Biosample	env_broad_scale	range	ControlledIdentifiedTermValue
Biosample	env_local_scale	range	ControlledIdentifiedTermValue
Biosample	env_medium	range	ControlledIdentifiedTermValue
Biosample	samp_taxon_id	range	ControlledIdentifiedTermValue
GenomeFeature	feature_category	range	ControlledIdentifiedTermValue
FunctionalAnnotation	feature_category	range	ControlledIdentifiedTermValue

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: ControlledIdentifiedTermValue
description: A controlled term or class from an ontology, requiring the presence of
  term with an id
notes:
- To be used for slots like env_broad_scale
from_schema: https://w3id.org/nmdc/nmdc
is_a: ControlledTermValue
slot_usage:
  term:
    name: term
    required: true
class_uri: nmdc:ControlledIdentifiedTermValue

Induced

name: ControlledIdentifiedTermValue
description: A controlled term or class from an ontology, requiring the presence of
  term with an id
notes:
- To be used for slots like env_broad_scale
from_schema: https://w3id.org/nmdc/nmdc
is_a: ControlledTermValue
slot_usage:
  term:
    name: term
    required: true
attributes:
  term:
    name: term
    description: pointer to an ontology class
    notes:
    - 'removed ''slot_uri: rdf:type'''
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: term
    owner: ControlledIdentifiedTermValue
    domain_of:
    - ControlledTermValue
    range: OntologyClass
    required: true
    inlined: true
  has_raw_value:
    name: has_raw_value
    description: The value that was specified for an annotation in raw form, i.e.
      a string. E.g. "2 cm" or "2-4 cm"
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: has_raw_value
    owner: ControlledIdentifiedTermValue
    domain_of:
    - AttributeValue
    range: string
  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: ControlledIdentifiedTermValue
    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:ControlledIdentifiedTermValue