Class: OrganismTaxon
Description: 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.
Aliases: taxon, taxonomic classification
classDiagram
class OrganismTaxon
NamedThing <|-- OrganismTaxon
OrganismTaxon : category
OrganismTaxon : deprecated
OrganismTaxon : description
OrganismTaxon : full_name
OrganismTaxon : has_attribute
OrganismTaxon --|> Attribute : has_attribute
OrganismTaxon : has_taxonomic_rank
OrganismTaxon --|> TaxonomicRank : has_taxonomic_rank
OrganismTaxon : id
OrganismTaxon : iri
OrganismTaxon : name
OrganismTaxon : provided_by
OrganismTaxon : synonym
OrganismTaxon : type
OrganismTaxon : xref
Inheritance
- Entity
- NamedThing
- OrganismTaxon
- NamedThing
Slots
| Name | Cardinality and Range | Inheritance | Examples |
|---|---|---|---|
| has_taxonomic_rank: None |
0..1 TaxonomicRank |
direct | |
| provided_by: 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. |
0..* String |
NamedThing | |
| xref: 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. |
0..* Uriorcurie |
NamedThing | |
| full_name: a long-form human readable name for a thing |
0..1 LabelType |
NamedThing | |
| synonym: Alternate human-readable names for a thing |
0..* LabelType |
NamedThing | |
| id: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI |
1..1 String |
Entity | |
| iri: An IRI for an entity. This is determined by the id using expansion rules. |
0..1 IriType |
Entity | |
| category: 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} |
1..* Uriorcurie |
Entity | |
| type: None |
0..* String |
Entity | |
| name: A human-readable name for an attribute or entity. |
0..1 LabelType |
Entity | |
| description: a human-readable description of an entity |
0..1 NarrativeText |
Entity | |
| has_attribute: connects any entity to an attribute |
0..* Attribute |
Entity | |
| deprecated: A boolean flag indicating that an entity is no longer considered current or valid. |
0..1 Boolean |
Entity |
Usages
Valid ID Prefixes
Instances of this class should have identifiers with one of the following prefixes, ordered with the most preferred first:
LinkML Source
name: organism taxon
id_prefixes:
- NCBITaxon
- MESH
- UMLS
description: '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.'
in_subset:
- model_organism_database
from_schema: https://w3id.org/biolink/biolink-model
aliases:
- taxon
- taxonomic classification
exact_mappings:
- WIKIDATA:Q16521
- STY:T001
- bioschemas:Taxon
narrow_mappings:
- dcid:BiologicalSpecies
is_a: named thing
values_from:
- NCBITaxon
slots:
- has taxonomic rank
slot_usage:
has taxonomic rank:
name: has taxonomic rank
mappings:
- WIKIDATA:P105
multivalued: false
domain_of:
- organism taxon
range: taxonomic rank