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.
Identifier prefixes
- NCBITaxon
- MESH
- UMLS
Parents
- is_a: NamedThing - a databased entity or concept/class
Referenced by class
- ChemicalAffectsGeneAssociation species context qualifier 0..1 OrganismTaxon
- ThingWithTaxon in taxon 0..* OrganismTaxon
- OrganismTaxonToEntityAssociation subject 1..1 OrganismTaxon
- OrganismTaxonToEnvironmentAssociation subject 1..1 OrganismTaxon
- OrganismTaxonToOrganismTaxonAssociation object 1..1 OrganismTaxon
- OrganismTaxonToOrganismTaxonAssociation subject 1..1 OrganismTaxon
- OrganismTaxonToOrganismTaxonInteraction object 1..1 OrganismTaxon
- OrganismTaxonToOrganismTaxonInteraction subject 1..1 OrganismTaxon
- OrganismTaxonToOrganismTaxonSpecialization object 1..1 OrganismTaxon
- OrganismTaxonToOrganismTaxonSpecialization subject 1..1 OrganismTaxon
- Association species context qualifier 0..1 OrganismTaxon
- TaxonToTaxonAssociation object 1..1 OrganismTaxon
- TaxonToTaxonAssociation subject 1..1 OrganismTaxon
Attributes
Own
- 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 featuref
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..*
- Range: String
- description 0..1
- Description: a human-readable description of an entity
- Range: NarrativeText
- in subsets: (translator_minimal)
- has attribute 0..*
- Description: connects any entity to an attribute
- Range: Attribute
- in subsets: (samples)
Inherited from gene product mixin:
- xref 0..*
- Description: A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.
- Range: Uriorcurie
- in subsets: (translator_minimal)
Inherited from macromolecular machine mixin:
- name 0..1
- Description: A human-readable name for an attribute or entity.
- Range: LabelType
- in subsets: (translator_minimal,samples)
Inherited from named thing:
- provided by 0..*
- Description: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
- Range: String
- 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 featuref
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)
Domain for slot:
- has taxonomic rank 0..1
- Range: TaxonomicRank
Other properties
Aliases: | taxon | |
taxonomic classification | ||
In Subsets: | model_organism_database | |
Exact Mappings: | WIKIDATA:Q16521 | |
STY:T001 | ||
bioschemas:Taxon | ||
Narrow Mappings: | dcid:BiologicalSpecies |