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: NamedThing - a databased entity or concept/class

Children

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

Referenced by class

• ThingWithTaxon in taxon _0..* OrganismTaxon
• OrganismTaxonToEntityAssociation organism taxon to entity association➞subject _REQ OrganismTaxon
• OrganismTaxonToEnvironmentAssociation organism taxon to environment association➞subject _REQ OrganismTaxon
• OrganismTaxonToOrganismTaxonAssociation organism taxon to organism taxon association➞object _REQ OrganismTaxon
• OrganismTaxonToOrganismTaxonAssociation organism taxon to organism taxon association➞subject _REQ OrganismTaxon
• OrganismTaxonToOrganismTaxonInteraction organism taxon to organism taxon interaction➞object _REQ OrganismTaxon
• OrganismTaxonToOrganismTaxonInteraction organism taxon to organism taxon interaction➞subject _REQ OrganismTaxon
• OrganismTaxonToOrganismTaxonSpecialization organism taxon to organism taxon specialization➞object _REQ OrganismTaxon
• OrganismTaxonToOrganismTaxonSpecialization organism taxon to organism taxon specialization➞subject _REQ OrganismTaxon
• OrganismTaxon organism taxon➞subclass of _0..* OrganismTaxon

Attributes

Own

• organism taxon➞has taxonomic rank _OPT
  • range: TaxonomicRank
• organism taxon➞subclass of _0..*
  • Description: subclass of holds between two taxa, e.g. human subclass of mammal
  • range: OrganismTaxon

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 _0..*
  • 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 biolink:Protein, biolink:GeneProduct, biolink: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 {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}
  • range: CategoryType
  • in subsets: (translator_minimal)
• type _OPT
  • range: String
• 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:

• named thing➞category _1..*
  • range: NamedThing

Domain for slot:

• organism taxon➞has taxonomic rank _OPT
  • range: TaxonomicRank
• organism taxon➞subclass of _0..*
  • Description: subclass of holds between two taxa, e.g. human subclass of mammal
  • range: OrganismTaxon

Other properties