Class: GeneFamily
Description: any grouping of multiple genes or gene products related by common descent
Aliases: orthogroup, protein family
classDiagram
class GeneFamily
GeneGroupingMixin <|-- GeneFamily
ChemicalEntityOrGeneOrGeneProduct <|-- GeneFamily
BiologicalEntity <|-- GeneFamily
GeneFamily : category
GeneFamily : deprecated
GeneFamily : description
GeneFamily : full_name
GeneFamily : has_attribute
GeneFamily --|> Attribute : has_attribute
GeneFamily : has_gene_or_gene_product
GeneFamily --|> Gene : has_gene_or_gene_product
GeneFamily : id
GeneFamily : in_taxon
GeneFamily --|> OrganismTaxon : in_taxon
GeneFamily : in_taxon_label
GeneFamily : iri
GeneFamily : name
GeneFamily : provided_by
GeneFamily : synonym
GeneFamily : type
GeneFamily : xref
Inheritance
Slots
| Name | Cardinality and Range | Inheritance | Examples |
|---|---|---|---|
| has_gene_or_gene_product: connects an entity with one or more gene or gene products |
* Gene |
GeneGroupingMixin | |
| 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 | |
| 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 |
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 | |
| id: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI |
1 String |
Entity | |
| 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: A human-readable name for an attribute or entity. |
0..1 LabelType |
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 |
|---|---|---|---|
| GeneToGeneFamilyAssociation | object | range | GeneFamily |
Valid ID Prefixes
Instances of this class should have identifiers with one of the following prefixes, ordered with the most preferred first:
| ID Prefix | Usage |
|---|---|
| PANTHER.FAMILY | GeneFamily |
| HGNC.FAMILY | GeneFamily |
| FB | Pathway Gene Transcript Polypeptide Protein GeneFamily Genotype SequenceVariant |
| interpro | GeneFamily |
| CATH | GeneFamily |
| CDD | GeneFamily |
| HAMAP | GeneFamily |
| PFAM | GeneFamily |
| PIRSF | GeneFamily |
| PRINTS | GeneFamily |
| PRODOM | GeneFamily |
| PROSITE | GeneFamily |
| SMART | GeneFamily |
| SUPFAM | GeneFamily |
| TIGRFAM | GeneFamily |
| CATH.SUPERFAMILY | GeneFamily |
| RFAM | GeneFamily |
| KEGG.ORTHOLOGY | MolecularActivity GeneFamily |
| EGGNOG | GeneFamily |
| COG | GeneFamily |
LinkML Source
name: gene family
id_prefixes:
- PANTHER.FAMILY
- HGNC.FAMILY
- FB
- interpro
- CATH
- CDD
- HAMAP
- PFAM
- PIRSF
- PRINTS
- PRODOM
- PROSITE
- SMART
- SUPFAM
- TIGRFAM
- CATH.SUPERFAMILY
- RFAM
- KEGG.ORTHOLOGY
- EGGNOG
- COG
description: any grouping of multiple genes or gene products related by common descent
in_subset:
- model_organism_database
from_schema: https://w3id.org/biolink/biolink-model
aliases:
- orthogroup
- protein family
exact_mappings:
- NCIT:C26004
- WIKIDATA:Q2278983
narrow_mappings:
- SIO:001380
- NCIT:C20130
- WIKIDATA:Q417841
is_a: biological entity
mixins:
- gene grouping mixin
- chemical entity or gene or gene product