biolink-model

Class: Polypeptide

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.

URI: biolink:Polypeptide

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Identifier prefixes

• UniProtKB
• PR
• ENSEMBL
• FB
• UMLS

Parents

• is_a: BiologicalEntity

Uses Mixins

• mixin: ChemicalEntityOrGeneOrGeneProduct - A union of chemical entities and children, and gene or gene product. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities.
• mixin: ChemicalEntityOrProteinOrPolypeptide - A union of chemical entities and children, and protein and polypeptide. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities.

Children

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

Referenced by class

Attributes

Inherited from entity:

• id _1..1
  • Description: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI
  • Range: String
  • in subsets: (translator_minimal)
• iri _0..1
  • Description: An IRI for an entity. This is determined by the id using expansion rules.
  • Range: IriType
  • in subsets: (translator_minimal,samples)
• category _0..*
  • Description: 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}
  • Range: CategoryType
  • in subsets: (translator_minimal)
• type _0..*
  • Range: String
• description _0..1
  • Description: a human-readable description of an entity
  • Range: NarrativeText
  • in subsets: (translator_minimal)
• has attribute _0..*
  • Description: connects any entity to an attribute
  • Range: Attribute
  • in subsets: (samples)

Inherited from gene product mixin:

• synonym _0..*
  • Description: Alternate human-readable names for a thing
  • Range: LabelType
  • in subsets: (translator_minimal)
• xref _0..*
  • Description: 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.
  • Range: Uriorcurie
  • in subsets: (translator_minimal)

Inherited from macromolecular machine mixin:

• name _0..1
  • Description: A human-readable name for an attribute or entity.
  • Range: LabelType
  • in subsets: (translator_minimal,samples)

Inherited from named thing:

• provided by _0..*
  • Description: 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.
  • Range: String
• full name _0..1
  • Description: a long-form human readable name for a thing
  • Range: LabelType
• category _0..*
  • Description: 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}
  • Range: CategoryType
  • in subsets: (translator_minimal)

Inherited from thing with taxon:

• in taxon _0..*
  • Description: connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see ‘thing with taxon’
  • Range: OrganismTaxon
  • in subsets: (translator_minimal)
• in taxon label _0..1
  • Description: The human readable scientific name for the taxon of the entity.
  • Range: LabelType
  • in subsets: (translator_minimal)

Other properties

Aliases:		amino acid entity
In Subsets:		model_organism_database
Narrow Mappings:		SO:0000104
		STY:T116
		STY:T087

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