Class: Gene
Description: 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
class Gene
GeneOrGeneProduct <|-- Gene
GenomicEntity <|-- Gene
ChemicalEntityOrGeneOrGeneProduct <|-- Gene
PhysicalEssence <|-- Gene
OntologyClass <|-- Gene
BiologicalEntity <|-- Gene
Gene : category
Gene : deprecated
Gene : description
Gene : full_name
Gene : has_attribute
Gene --|> Attribute : has_attribute
Gene : has_biological_sequence
Gene : id
Gene : in_taxon
Gene --|> OrganismTaxon : in_taxon
Gene : in_taxon_label
Gene : iri
Gene : name
Gene : provided_by
Gene : symbol
Gene : synonym
Gene : type
Gene : xref
Inheritance
Slots
| Name | Cardinality and Range | Inheritance | Examples |
|---|---|---|---|
| symbol: Symbol for a particular thing |
0..1 String |
direct | |
| xref: A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references. |
* Uriorcurie |
direct | |
| has_biological_sequence: connects a genomic feature to its sequence |
0..1 BiologicalSequence |
GenomicEntity | |
| id: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI |
1 String |
OntologyClass, Entity | |
| in_taxon: connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon' |
* OrganismTaxon |
ThingWithTaxon | |
| in_taxon_label: The human readable scientific name for the taxon of the entity. |
0..1 LabelType |
ThingWithTaxon | |
| 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. |
* String |
NamedThing | |
| full_name: a long-form human readable name for a thing |
0..1 LabelType |
NamedThing | |
| synonym: Alternate human-readable names for a thing |
* LabelType |
NamedThing | |
| iri: An IRI for an entity. This is determined by the id using expansion rules. |
0..1 IriType |
Entity | |
| 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. 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} |
1..* Uriorcurie |
Entity | |
| type: None |
* String |
Entity | |
| name: 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 |
0..1 SymbolType |
MacromolecularMachineMixin, Entity | |
| description: a human-readable description of an entity |
0..1 NarrativeText |
Entity | |
| has_attribute: connects any entity to an attribute |
* Attribute |
Entity | |
| deprecated: A boolean flag indicating that an entity is no longer considered current or valid. |
0..1 Boolean |
Entity |
Usages
| used by | used in | type | used |
|---|---|---|---|
| ProteinDomain | has_gene_or_gene_product | range | Gene |
| ProteinFamily | has_gene_or_gene_product | range | Gene |
| GeneGroupingMixin | has_gene_or_gene_product | range | Gene |
| GeneFamily | has_gene_or_gene_product | range | Gene |
| SequenceVariant | has_gene | range | Gene |
| Snv | has_gene | range | Gene |
| GenomicBackgroundExposure | has_gene_or_gene_product | range | Gene |
| DrugToGeneInteractionExposure | has_gene_or_gene_product | range | Gene |
| GenotypeToGeneAssociation | object | range | Gene |
| GeneToGeneFamilyAssociation | subject | range | Gene |
| VariantToGeneAssociation | object | range | Gene |
| VariantToGeneExpressionAssociation | object | range | Gene |
| GeneToGoTermAssociation | subject | range | Gene |
| TranscriptToGeneRelationship | object | range | Gene |
| GeneToGeneProductRelationship | subject | range | Gene |
Valid ID Prefixes
Instances of this class should have identifiers with one of the following prefixes, ordered with the most preferred first:
LinkML Source
name: gene
id_prefixes:
- NCBIGene
- ENSEMBL
- HGNC
- MGI
- ZFIN
- dictyBase
- WB
- WormBase
- FB
- RGD
- SGD
- PomBase
- OMIM
- KEGG.GENES
- UMLS
- Xenbase
- AspGD
- PHARMGKB.GENE
description: 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.
in_subset:
- translator_minimal
- model_organism_database
from_schema: https://w3id.org/biolink/biolink-model
exact_mappings:
- SO:0000704
- SIO:010035
- WIKIDATA:Q7187
- dcid:Gene
narrow_mappings:
- bioschemas:gene
broad_mappings:
- NCIT:C45822
is_a: biological entity
mixins:
- gene or gene product
- genomic entity
- chemical entity or gene or gene product
- physical essence
- ontology class
slots:
- symbol
- xref