BiologicalEntity

None

classDiagram ThingWithTaxon <|-- BiologicalEntity NamedThing <|-- BiologicalEntity BiologicalEntity : category BiologicalEntity : description BiologicalEntity : has_attribute BiologicalEntity : id BiologicalEntity : in_taxon BiologicalEntity : iri BiologicalEntity : name BiologicalEntity : provided_by BiologicalEntity : source BiologicalEntity : type BiologicalEntity : xref

Parent Classes

Entity
- NamedThing
  - BiologicalEntity [ thing with taxon]
    - BiologicalProcessOrActivity [ occurrent ontology class]
    - OrganismalEntity
    - DiseaseOrPhenotypicFeature [ thing with taxon]
    - Gene [ gene or gene product genomic entity chemical entity or gene or gene product physical essence ontology class]
    - Genome [ genomic entity physical essence ontology class]
    - Polypeptide [ chemical entity or gene or gene product chemical entity or protein or polypeptide]
    - ProteinDomain [ gene grouping mixin chemical entity or gene or gene product]
    - ProteinFamily [ gene grouping mixin chemical entity or gene or gene product]
    - NucleicAcidSequenceMotif
    - GeneFamily [ gene grouping mixin chemical entity or gene or gene product]
    - Genotype [ physical essence genomic entity ontology class]
    - Haplotype [ genomic entity physical essence ontology class]
    - SequenceVariant [ genomic entity physical essence ontology class]
    - ReagentTargetedGene [ genomic entity physical essence ontology class]

Children

Entity
- NamedThing
  - BiologicalEntity [ thing with taxon]
    - BiologicalProcessOrActivity [ occurrent ontology class]
    - OrganismalEntity
    - DiseaseOrPhenotypicFeature [ thing with taxon]
    - Gene [ gene or gene product genomic entity chemical entity or gene or gene product physical essence ontology class]
    - Genome [ genomic entity physical essence ontology class]
    - Polypeptide [ chemical entity or gene or gene product chemical entity or protein or polypeptide]
    - ProteinDomain [ gene grouping mixin chemical entity or gene or gene product]
    - ProteinFamily [ gene grouping mixin chemical entity or gene or gene product]
    - NucleicAcidSequenceMotif
    - GeneFamily [ gene grouping mixin chemical entity or gene or gene product]
    - Genotype [ physical essence genomic entity ontology class]
    - Haplotype [ genomic entity physical essence ontology class]
    - SequenceVariant [ genomic entity physical essence ontology class]
    - ReagentTargetedGene [ genomic entity physical essence ontology class]

Slots

Name	Description
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`, etc. 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}
description	a human-readable description of an entity
has_attribute	connects any entity to an attribute
id	A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI
in_taxon	connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'
iri	An IRI for an entity. This is determined by the id using expansion rules.
name	A human-readable name for an attribute or entity.
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.
source	None
type	None
xref	Alternate CURIEs for a thing

Mappings

Mapping Type	Mapped Value
self	['https://w3id.org/biolink/biolink-model/:BiologicalEntity']
native	['https://w3id.org/biolink/biolink-model/:BiologicalEntity']
narrow	['WIKIDATA:Q28845870', 'STY:T050', 'SIO:010046']