Class: Polypeptide

Description: A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule.

Aliases: amino acid entity

classDiagram class Polypeptide ChemicalEntityOrGeneOrGeneProduct <|-- Polypeptide ChemicalEntityOrProteinOrPolypeptide <|-- Polypeptide BiologicalEntity <|-- Polypeptide Polypeptide <|-- Protein Polypeptide : category Polypeptide : deprecated Polypeptide : description Polypeptide : full_name Polypeptide : has_attribute Polypeptide --|> Attribute : has_attribute Polypeptide : id Polypeptide : in_taxon Polypeptide --|> OrganismTaxon : in_taxon Polypeptide : in_taxon_label Polypeptide : iri Polypeptide : name Polypeptide : provided_by Polypeptide : synonym Polypeptide : type Polypeptide : xref

Inheritance

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

Slots

Name	Cardinality and Range	Inheritance
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

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 ProcessedMaterial Drug EnvironmentalFoodContaminant FoodAdditive Food Disease PhenotypicFeature AnatomicalEntity CellularComponent Cell GrossAnatomicalStructure Gene Polypeptide Protein

LinkML Source

name: polypeptide
id_prefixes:
- UniProtKB
- PR
- ENSEMBL
- FB
- UMLS
description: A polypeptide is a molecular entity characterized by availability in
  protein databases of amino-acid-based sequence representations of its precise primary
  structure; for convenience of representation, partial sequences of various kinds
  are included, even if they do not represent a physical molecule.
in_subset:
- model_organism_database
from_schema: https://w3id.org/biolink/biolink-model
aliases:
- amino acid entity
narrow_mappings:
- SO:0000104
- STY:T116
- STY:T087
is_a: biological entity
mixins:
- chemical entity or gene or gene product
- chemical entity or protein or polypeptide