Class: Protein

Description: A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA

classDiagram class Protein GeneProductMixin <|-- Protein Polypeptide <|-- Protein Protein <|-- ProteinIsoform Protein : category Protein : deprecated Protein : description Protein : equivalent_identifiers Protein : full_name Protein : has_attribute Protein --|> Attribute : has_attribute Protein : id Protein : in_taxon Protein --|> OrganismTaxon : in_taxon Protein : in_taxon_label Protein : information_content Protein : iri Protein : name Protein : provided_by Protein : synonym Protein : type Protein : xref

Inheritance

Entity
- NamedThing
  - BiologicalEntity [ ThingWithTaxon]
    - Polypeptide [ ChemicalEntityOrGeneOrGeneProduct ChemicalEntityOrProteinOrPolypeptide]
      - Protein [ GeneProductMixin]
        
        ProteinIsoform [ GeneProductIsoformMixin]

Slots

Name	Cardinality and Range	Inheritance
synonym: Alternate human-readable names for a thing	* LabelType	GeneProductMixin, 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	GeneProductMixin, NamedThing
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
information_content: Information content (IC) value for a term, primarily from Automats.	0..1 Float	NamedThing
equivalent_identifiers: A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources.	* Uriorcurie	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: 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	Entity, MacromolecularMachineMixin
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

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
UniProtKB	GeneProductMixin Polypeptide Protein ProteinIsoform
PR	GeneProductMixin MacromolecularComplex Polypeptide Protein ProteinIsoform
ENSEMBL	Gene Transcript Polypeptide Protein ProteinIsoform NoncodingRNAProduct
FB	Pathway Gene Transcript Polypeptide Protein GeneFamily Genotype SequenceVariant
UMLS	OntologyClass OrganismTaxon MolecularEntity ChemicalEntity SmallMolecule ChemicalMixture NucleicAcidEntity MolecularMixture ComplexMolecularMixture MolecularActivity BiologicalProcess ProcessedMaterial Drug EnvironmentalFoodContaminant FoodAdditive Food Disease PhenotypicFeature AnatomicalEntity CellularComponent Cell GrossAnatomicalStructure Gene Polypeptide Protein
MESH	OntologyClass OrganismTaxon MolecularEntity ChemicalEntity SmallMolecule ChemicalMixture NucleicAcidEntity MolecularMixture ComplexMolecularMixture ProcessedMaterial Drug EnvironmentalFoodContaminant FoodAdditive Food Disease PhenotypicFeature AnatomicalEntity CellularComponent Cell GrossAnatomicalStructure Protein
ncats.drug	Drug Protein

LinkML Source

name: protein
id_prefixes:
- UniProtKB
- PR
- ENSEMBL
- FB
- UMLS
- MESH
- ncats.drug
description: A gene product that is composed of a chain of amino acid sequences and
  is produced by ribosome-mediated translation of mRNA
from_schema: https://w3id.org/biolink/biolink-model
exact_mappings:
- PR:000000001
- SIO:010043
- WIKIDATA:Q8054
narrow_mappings:
- STY:T126
- STY:T192
broad_mappings:
- bioschemas:Protein
is_a: polypeptide
mixins:
- gene product mixin