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Class: NcbiTaxon

A taxonomy term from NCBI Taxonomy. NcbiTaxon instances are identified by NCBITaxon CURIEs (e.g. NCBITaxon:511145) and stored in ontology_class_set alongside other OntologyClass instances. No NMDC-minted identifiers are assigned. Support for additional taxonomic authorities (GTDB, LPSN, SeqCode) would be represented by separate classes or by widening this class's id_prefixes in a follow-on PR.

URI: nmdc:NcbiTaxon

classDiagram class NcbiTaxon click NcbiTaxon href "../NcbiTaxon" OntologyClass <|-- NcbiTaxon click OntologyClass href "../OntologyClass" NcbiTaxon : alternative_identifiers NcbiTaxon : alternative_names NcbiTaxon : definition NcbiTaxon : description NcbiTaxon : id NcbiTaxon : is_obsolete NcbiTaxon : is_root NcbiTaxon : name NcbiTaxon : relations NcbiTaxon --> "*" OntologyRelation : relations click OntologyRelation href "../OntologyRelation" NcbiTaxon : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
alternative_names *
String		 A list of alternative names used to refer to the entity OntologyClass
relations *
OntologyRelation		 OntologyClass
definition 0..1
String		 The definition of the ontology term as provided by the ontology OntologyClass
is_obsolete 0..1
Boolean		 A boolean value indicating whether the ontology term is obsolete OntologyClass
is_root 0..1
Boolean		 A boolean value indicating whether the ontology term is a root term; it is no... 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

Comments

  • Follows the OrthologyGroup pattern: a concrete, directly-instantiated semantic subclass of OntologyClass with no additional slots, no typecode, and no dedicated Database collection. Instances go into ontology_class_set and are referenced from sample slots such as classified_as.
  • Sub-species information (strains, cultivars, lab-specific isolates) is below the resolution of NCBI Taxonomy. Strain identity should be captured via dedicated text slots on OrganismSample (e.g. isolate_name, source_mat_id, subspecf_gen_lin) or a future Strain class — not by minting NcbiTaxon instances for strains.
  • Existing taxonomy slots (samp_taxon_id, host_taxid) already use ControlledIdentifiedTermValue with range OntologyClass. The intent is that these slots point to NcbiTaxon instances specifically, but LinkML does not currently support constraining the term slot of a ControlledIdentifiedTermValue to a particular OntologyClass subclass.

See Also

Identifier and Mapping Information

Valid ID Prefixes

Instances of this class should have identifiers with one of the following prefixes:

  • NCBITaxon

Schema Source

Mappings

Mapping Type Mapped Value
close biolink:OrganismTaxon

LinkML Source

Direct

name: NcbiTaxon
id_prefixes:
- NCBITaxon
description: A taxonomy term from NCBI Taxonomy. NcbiTaxon instances are identified
  by NCBITaxon CURIEs (e.g. NCBITaxon:511145) and stored in ontology_class_set alongside
  other OntologyClass instances. No NMDC-minted identifiers are assigned. Support
  for additional taxonomic authorities (GTDB, LPSN, SeqCode) would be represented
  by separate classes or by widening this class's id_prefixes in a follow-on PR.
comments:
- 'Follows the OrthologyGroup pattern: a concrete, directly-instantiated semantic
  subclass of OntologyClass with no additional slots, no typecode, and no dedicated
  Database collection. Instances go into ontology_class_set and are referenced from
  sample slots such as classified_as.'
- Sub-species information (strains, cultivars, lab-specific isolates) is below the
  resolution of NCBI Taxonomy. Strain identity should be captured via dedicated text
  slots on OrganismSample (e.g. isolate_name, source_mat_id, subspecf_gen_lin) or
  a future Strain class — not by minting NcbiTaxon instances for strains.
- Existing taxonomy slots (samp_taxon_id, host_taxid) already use ControlledIdentifiedTermValue
  with range OntologyClass. The intent is that these slots point to NcbiTaxon instances
  specifically, but LinkML does not currently support constraining the term slot of
  a ControlledIdentifiedTermValue to a particular OntologyClass subclass.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://github.com/microbiomedata/nmdc-schema/issues/2959
- https://github.com/microbiomedata/nmdc-schema/issues/2971
close_mappings:
- biolink:OrganismTaxon
is_a: OntologyClass
slot_usage:
  id:
    name: id
    comments:
    - Validation is intentionally limited to NCBITaxon CURIEs. If GTDB, LPSN, or SeqCode
      support is added, widen this pattern in lockstep with id_prefixes and example
      data.
    pattern: ^NCBITaxon:\d+$
class_uri: nmdc:NcbiTaxon

Induced

name: NcbiTaxon
id_prefixes:
- NCBITaxon
description: A taxonomy term from NCBI Taxonomy. NcbiTaxon instances are identified
  by NCBITaxon CURIEs (e.g. NCBITaxon:511145) and stored in ontology_class_set alongside
  other OntologyClass instances. No NMDC-minted identifiers are assigned. Support
  for additional taxonomic authorities (GTDB, LPSN, SeqCode) would be represented
  by separate classes or by widening this class's id_prefixes in a follow-on PR.
comments:
- 'Follows the OrthologyGroup pattern: a concrete, directly-instantiated semantic
  subclass of OntologyClass with no additional slots, no typecode, and no dedicated
  Database collection. Instances go into ontology_class_set and are referenced from
  sample slots such as classified_as.'
- Sub-species information (strains, cultivars, lab-specific isolates) is below the
  resolution of NCBI Taxonomy. Strain identity should be captured via dedicated text
  slots on OrganismSample (e.g. isolate_name, source_mat_id, subspecf_gen_lin) or
  a future Strain class — not by minting NcbiTaxon instances for strains.
- Existing taxonomy slots (samp_taxon_id, host_taxid) already use ControlledIdentifiedTermValue
  with range OntologyClass. The intent is that these slots point to NcbiTaxon instances
  specifically, but LinkML does not currently support constraining the term slot of
  a ControlledIdentifiedTermValue to a particular OntologyClass subclass.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://github.com/microbiomedata/nmdc-schema/issues/2959
- https://github.com/microbiomedata/nmdc-schema/issues/2971
close_mappings:
- biolink:OrganismTaxon
is_a: OntologyClass
slot_usage:
  id:
    name: id
    comments:
    - Validation is intentionally limited to NCBITaxon CURIEs. If GTDB, LPSN, or SeqCode
      support is added, widen this pattern in lockstep with id_prefixes and example
      data.
    pattern: ^NCBITaxon:\d+$
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.  This should not
      be used for identifers which have their own slots (e.g., bioproject:PRJNA406974)
    from_schema: https://w3id.org/nmdc/nmdc
    exact_mappings:
    - dcterms:alternative
    - skos:altLabel
    rank: 1000
    alias: alternative_names
    owner: NcbiTaxon
    domain_of:
    - OntologyClass
    - Study
    - Biosample
    range: string
    multivalued: true
  relations:
    name: relations
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: relations
    owner: NcbiTaxon
    domain_of:
    - OntologyClass
    range: OntologyRelation
    multivalued: true
    inlined: true
    inlined_as_list: true
  definition:
    name: definition
    description: The definition of the ontology term as provided by the ontology.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: definition
    owner: NcbiTaxon
    domain_of:
    - OntologyClass
    range: string
  is_obsolete:
    name: is_obsolete
    description: A boolean value indicating whether the ontology term is obsolete.
    comments:
    - If true (the ontology term is declared obsolete via the ontology source itself),
      the term is no longer considered a valid term to use in an annotation at NMDC,
      and it no longer has ontology_relation_set records.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: is_obsolete
    owner: NcbiTaxon
    domain_of:
    - OntologyClass
    range: boolean
  is_root:
    name: is_root
    description: A boolean value indicating whether the ontology term is a root term;
      it is not a subclass of  any other term.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: is_root
    owner: NcbiTaxon
    domain_of:
    - OntologyClass
    range: boolean
  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
    comments:
    - Validation is intentionally limited to NCBITaxon CURIEs. If GTDB, LPSN, or SeqCode
      support is added, widen this pattern in lockstep with id_prefixes and example
      data.
    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
    structured_aliases:
    - literal_form: workflow_execution_id
      predicate: NARROW_SYNONYM
      contexts:
      - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
    - literal_form: data_object_id
      predicate: NARROW_SYNONYM
      contexts:
      - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
    rank: 1000
    identifier: true
    alias: id
    owner: NcbiTaxon
    domain_of:
    - NamedThing
    range: uriorcurie
    required: true
    pattern: ^NCBITaxon:\d+$
  name:
    name: name
    description: A human readable label for an entity
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: name
    owner: NcbiTaxon
    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: NcbiTaxon
    domain_of:
    - ImageValue
    - NamedThing
    - Protocol
    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: NcbiTaxon
    domain_of:
    - NamedThing
    - MetaboliteIdentification
    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:
    - 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
    structured_aliases:
    - literal_form: workflow_execution_class
      predicate: NARROW_SYNONYM
      contexts:
      - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
    rank: 1000
    slot_uri: rdf:type
    designates_type: true
    alias: type
    owner: NcbiTaxon
    domain_of:
    - EukEval
    - FunctionalAnnotationAggMember
    - PeptideQuantification
    - ProteinQuantification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - OntologyRelation
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    - ProvenanceMetadata
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    range: uriorcurie
    required: true
class_uri: nmdc:NcbiTaxon