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Class: ProteinDomain

Description: A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain.
classDiagram class ProteinDomain GeneGroupingMixin <|-- ProteinDomain ChemicalEntityOrGeneOrGeneProduct <|-- ProteinDomain BiologicalEntity <|-- ProteinDomain ProteinDomain : category ProteinDomain : deprecated ProteinDomain : description ProteinDomain : full_name ProteinDomain : has_attribute ProteinDomain --|> Attribute : has_attribute ProteinDomain : has_gene_or_gene_product ProteinDomain --|> Gene : has_gene_or_gene_product ProteinDomain : id ProteinDomain : in_taxon ProteinDomain --|> OrganismTaxon : in_taxon ProteinDomain : in_taxon_label ProteinDomain : iri ProteinDomain : name ProteinDomain : provided_by ProteinDomain : synonym ProteinDomain : type ProteinDomain : 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
0..*
Gene		 GeneGroupingMixin
in_taxon:
connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon' 		0..*
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. 		0..*
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. 		0..*
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 		0..*
LabelType		 NamedThing
id:
A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI 		1..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 		0..*
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 		0..*
Attribute		 Entity
deprecated:
A boolean flag indicating that an entity is no longer considered current or valid. 		0..1
Boolean		 Entity

LinkML Source

name: protein domain
description: A conserved part of protein sequence and (tertiary) structure that can
  evolve, function, and exist independently of the rest of the protein chain. Protein
  domains maintain their structure and function independently of the proteins in which
  they are found. e.g. an SH3 domain.
from_schema: https://w3id.org/biolink/biolink-model
exact_mappings:
- NCIT:C13379
- SIO:001379
- UMLS:C1514562
is_a: biological entity
mixins:
- gene grouping mixin
- chemical entity or gene or gene product