Link

Class: OrganismTaxon

A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies.

URI: biolink:OrganismTaxon


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Identifier prefixes

  • NCBITaxon
  • MESH

Parents

  • is_a: OntologyClass - a concept or class in an ontology, vocabulary or thesaurus

Children

  • BioticExposure - An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses).

Referenced by class

Attributes

Own

Inherited from entity:

  • id REQ
    • Description: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI
    • range: String
    • in subsets: (translator_minimal)
  • iri OPT
    • Description: An IRI for an entity. This is determined by the id using expansion rules.
    • range: IriType
    • in subsets: (translator_minimal,samples)
  • category 1..*
    • Description: Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.
  • In a neo4j database this MAY correspond to the neo4j label tag.
  • In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values bl:Protein, bl:GeneProduct, bl:MolecularEntity, … In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature f may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {bl:GenomicEntity, bl:MolecularEntity, bl:NamedThing}
  • type OPT
  • description OPT
    • Description: a human-readable description of an entity
    • range: NarrativeText
    • in subsets: (translator_minimal)
  • source OPT
    • Description: a lightweight analog to the association class ‘has provider’ slot, which is the string name, or the authoritative (i.e. database) namespace, designating the origin of the entity to which the slot belongs.
    • range: LabelType
    • in subsets: (translator_minimal)
  • provided by 0..*
    • Description: connects an association to the agent (person, organization or group) that provided it
    • range: Agent
  • has attribute 0..*
    • Description: connects any entity to an attribute
    • range: Attribute
    • in subsets: (samples)

Inherited from macromolecular machine mixin:

  • macromolecular machine mixin➞name OPT
    • Description: genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name
    • range: SymbolType

Inherited from named thing:

Domain for slot:

Other properties

     
Aliases:   taxon
    taxonomic classification
In Subsets:   model_organism_database
Exact Mappings:   WIKIDATA:Q16521
Narrow Mappings:   UMLSSC:T005
    UMLSST:virs
    UMLSSC:T007
    UMLSST:bact
    UMLSSC:T194
    UMLSST:arch
    UMLSSC:T204
    UMLSST:euka
    UMLSSC:T002
    UMLSST:plnt
    UMLSSC:T004
    UMLSST:fngs
    UMLSSC:T008
    UMLSST:anim
    UMLSSC:T010
    UMLSST:vtbt
    UMLSSC:T011
    UMLSST:amph
    UMLSSC:T012
    UMLSST:bird
    UMLSSC:T013
    UMLSST:fish
    UMLSSC:T014
    UMLSST:rept
    UMLSSC:T015
    UMLSST:mamm
    UMLSSC:T016
    UMLSST:humn