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
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 featuref
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
Aliases: | locus | |
In Subsets: | model_organism_database | |
Exact Mappings: | SO:0000704 | |
SIO:010035 | ||
WIKIDATA:Q7187 |