Class: 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.

URI: biolink:Gene

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Identifier prefixes

• NCBIGENE
• ENSEMBL
• HGNC
• UniProtKB
• MGI
• ZFIN
• dictyBase
• WB
• WormBase
• FB
• FB
• RGD
• SGD
• POMBASE
• KEGG.GENE

Parents

• is_a: GenomicEntity - an entity that can either be directly located on a genome (gene, transcript, exon, regulatory region) or is encoded in a genome (protein)

Uses Mixins

• mixin: GeneOrGeneProduct - A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another

Referenced by class

• DiseaseOrPhenotypicFeature condition associated with gene _0..* Gene
• GeneToGeneProductRelationship gene to gene product relationship➞subject _REQ Gene
• Gene genetically interacts with _0..* Gene
• GenotypeToGeneAssociation genotype to gene association➞object _REQ Gene
• NamedThing has gene _0..* Gene
• NamedThing has gene or gene product _0..* Gene
• SequenceVariant is frameshift variant of _0..* Gene
• SequenceVariant is missense variant of _0..* Gene
• SequenceVariant is nearby variant of _0..* Gene
• SequenceVariant is non coding variant of _0..* Gene
• SequenceVariant is nonsense variant of _0..* Gene
• SequenceVariant is splice site variant of _0..* Gene
• SequenceVariant is synonymous variant of _0..* Gene
• SequenceVariant sequence variant➞has gene _0..* Gene
• TranscriptToGeneRelationship transcript to gene relationship➞object _REQ Gene
• VariantToGeneAssociation variant to gene association➞object _REQ Gene

Attributes

Inherited from entity:

• id _REQ
  • 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 _OPT
  • Description: An IRI for an entity. This is determined by the id using expansion rules.
  • range: IriType
  • in subsets: (translator_minimal,samples)
• 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 bl:Protein, bl:GeneProduct, bl: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 {bl:GenomicEntity, bl:MolecularEntity, bl:NamedThing}
  • range: CategoryType
  • in subsets: (translator_minimal)
• type _OPT
  • range: String
• description _OPT
  • Description: a human-readable description of an entity
  • range: NarrativeText
  • in subsets: (translator_minimal)
• source _OPT
  • 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 genomic entity:

• has biological sequence _OPT
  • Description: connects a genomic feature to its sequence
  • range: BiologicalSequence

Inherited from macromolecular machine mixin:

• macromolecular machine mixin➞name _OPT
  • 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

Inherited from named thing:

• named thing➞category _1..*
  • range: NamedThing

Inherited from thing with taxon:

• in taxon _0..*
  • Description: connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see ‘thing with taxon’
  • range: OrganismTaxon
  • in subsets: (translator_minimal)

Other properties