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
• MGI
• ZFIN
• dictyBase
• WB
• WormBase
• FB
• RGD
• SGD
• POMBASE
• OMIM
• KEGG.GENE
• UMLS
• Xenbase

Parents

• is_a: BiologicalEntity

Uses Mixins

• mixin: GeneOrGeneProduct - A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another
• mixin: GenomicEntity
• mixin: ChemicalEntityOrGeneOrGeneProduct - A union of chemical entities and children, and gene or gene product. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities.
• mixin: PhysicalEssence - Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge.
• mixin: OntologyClass - a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type.

Referenced by class

• DiseaseOrPhenotypicFeature condition associated with gene _0..* Gene
• GeneProductMixin gene product of _0..* Gene
• GeneToGeneProductRelationship gene to gene product relationship➞subject _1..1 Gene
• GeneToGoTermAssociation gene to go term association➞subject _1..1 Gene
• Gene genetically interacts with _0..* Gene
• GenotypeToGeneAssociation genotype to gene association➞object _1..1 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
• Transcript transcribed from _0..* Gene
• TranscriptToGeneRelationship transcript to gene relationship➞object _1..1 Gene
• VariantToGeneAssociation variant to gene association➞object _1..1 Gene

Attributes

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 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}
  • Range: CategoryType
  • in subsets: (translator_minimal)
• type _0..1
  • Range: String
• description _0..1
  • Description: a human-readable description of an entity
  • Range: NarrativeText
  • in subsets: (translator_minimal)
• source _0..1
  • 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 _0..1
  • Description: connects a genomic feature to its sequence
  • Range: BiologicalSequence

Inherited from macromolecular machine mixin:

• macromolecular machine mixin➞name _0..1
  • 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
  • in subsets: (translator_minimal,samples)

Inherited from named thing:

• named thing➞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 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}
  • Range: NamedThing
  • in subsets: (translator_minimal)

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