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Gene

A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions.

classDiagram GeneOrGeneProduct <|-- Gene GenomicEntity <|-- Gene ChemicalEntityOrGeneOrGeneProduct <|-- Gene PhysicalEssence <|-- Gene OntologyClass <|-- Gene BiologicalEntity <|-- Gene Gene : category Gene : description Gene : has_attribute Gene : has_biological_sequence Gene : id Gene : in_taxon Gene : iri Gene : name Gene : provided_by Gene : source Gene : symbol Gene : synonym Gene : type Gene : xref

Parent Classes

  • Entity
    • NamedThing
      • BiologicalEntity [ thing with taxon]
        • Gene [ gene or gene product genomic entity chemical entity or gene or gene product 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
has_biological_sequence connects a genomic feature to its sequence
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
symbol Symbol for a particular thing
synonym Alternate human-readable names for a thing
type None
xref Alternate CURIEs for a thing

Mappings

Mapping Type Mapped Value
self ['https://w3id.org/biolink/biolink-model/:Gene']
native ['https://w3id.org/biolink/biolink-model/:Gene']
exact ['SO:0000704', 'SIO:010035', 'WIKIDATA:Q7187', 'dcid:Gene']
narrow ['bioschemas:gene']
broad ['NCIT:C45822']