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

Referenced by class

• ThingWithTaxon in taxon _0..* OrganismTaxon
• OrganismTaxonToEntityAssociation organism taxon to entity association➞subject _1..1 OrganismTaxon
• OrganismTaxonToEnvironmentAssociation organism taxon to environment association➞subject _1..1 OrganismTaxon
• OrganismTaxonToOrganismTaxonAssociation organism taxon to organism taxon association➞object _1..1 OrganismTaxon
• OrganismTaxonToOrganismTaxonAssociation organism taxon to organism taxon association➞subject _1..1 OrganismTaxon
• OrganismTaxonToOrganismTaxonInteraction organism taxon to organism taxon interaction➞object _1..1 OrganismTaxon
• OrganismTaxonToOrganismTaxonInteraction organism taxon to organism taxon interaction➞subject _1..1 OrganismTaxon
• OrganismTaxonToOrganismTaxonSpecialization organism taxon to organism taxon specialization➞object _1..1 OrganismTaxon
• OrganismTaxonToOrganismTaxonSpecialization organism taxon to organism taxon specialization➞subject _1..1 OrganismTaxon
• TaxonToTaxonAssociation taxon to taxon association➞object _1..1 OrganismTaxon
• TaxonToTaxonAssociation taxon to taxon association➞subject _1..1 OrganismTaxon

Attributes

Own

• organism taxon➞has taxonomic rank _0..1
  • Range: TaxonomicRank

Inherited from entity:

• id _1..1
  • 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 _0..1
  • 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 _0..1
  • Range: String
• description _0..1
  • Description: a human-readable description of an entity
  • Range: NarrativeText
  • in subsets: (translator_minimal)
• source _0..1
  • 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 _0..1
  • 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
  • in subsets: (translator_minimal,samples)

Inherited from named thing:

• named thing➞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 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: NamedThing
  • in subsets: (translator_minimal)

Domain for slot:

• organism taxon➞has taxonomic rank _0..1
  • Range: TaxonomicRank

Other properties