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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

classDiagram class Gene GeneOrGeneProduct <|-- Gene GenomicEntity <|-- Gene ChemicalEntityOrGeneOrGeneProduct <|-- Gene PhysicalEssence <|-- Gene OntologyClass <|-- Gene BiologicalEntity <|-- Gene Gene : category Gene : description Gene : full_name Gene : has_attribute Gene --|> attribute : has_attribute Gene : has_biological_sequence Gene : id Gene : in_taxon Gene --|> organism taxon : 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 Description Inheritance
symbol 0..1
String		 Symbol for a particular thing direct
xref 0..*
Uriorcurie		 A database cross reference or alternative identifier for a NamedThing or edge... direct
has_biological_sequence 0..1
BiologicalSequence		 connects a genomic feature to its sequence GenomicEntity
id 1..1
String		 A unique identifier for an entity Entity, OntologyClass
in_taxon 0..*
OrganismTaxon		 connects an entity to its taxonomic classification ThingWithTaxon
in_taxon_label 0..1
LabelType		 The human readable scientific name for the taxon of the entity ThingWithTaxon
provided_by 0..*
String		 The value in this node property represents the knowledge provider that create... NamedThing
full_name 0..1
LabelType		 a long-form human readable name for a thing NamedThing
synonym 0..*
LabelType		 Alternate human-readable names for a thing NamedThing
iri 0..1
IriType		 An IRI for an entity Entity
category 1..*
CategoryType		 Name of the high level ontology class in which this entity is categorized Entity
type 0..*
String		 Entity
name 0..1
SymbolType		 genes are typically designated by a short symbol and a full name Entity, MacromolecularMachineMixin
description 0..1
NarrativeText		 a human-readable description of an entity Entity
has_attribute 0..*
Attribute		 connects any entity to an attribute 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

Identifier and Mapping Information

Valid ID Prefixes

Instances of this class should have identifiers with one of the following prefixes:

  • NCBIGene

  • ENSEMBL

  • HGNC

  • MGI

  • ZFIN

  • dictyBase

  • WB

  • WormBase

  • FB

  • RGD

  • SGD

  • PomBase

  • OMIM

  • KEGG.GENES

  • UMLS

  • Xenbase

  • AspGD

  • PHARMGKB.GENE

Schema Source

  • from schema: https://w3id.org/biolink/biolink-model

Mappings

Mapping Type Mapped Value
self biolink:Gene
native biolink:Gene
exact SO:0000704, SIO:010035, WIKIDATA:Q7187, dcid:Gene
narrow bioschemas:gene
broad NCIT:C45822

LinkML Source

Direct

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