Class: ProteinIsoform

Description: Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/

Aliases: proteoform

classDiagram class ProteinIsoform GeneProductIsoformMixin <|-- ProteinIsoform Protein <|-- ProteinIsoform ProteinIsoform : category ProteinIsoform : deprecated ProteinIsoform : description ProteinIsoform : full_name ProteinIsoform : has_attribute ProteinIsoform --|> Attribute : has_attribute ProteinIsoform : id ProteinIsoform : in_taxon ProteinIsoform --|> OrganismTaxon : in_taxon ProteinIsoform : in_taxon_label ProteinIsoform : iri ProteinIsoform : name ProteinIsoform : provided_by ProteinIsoform : synonym ProteinIsoform : type ProteinIsoform : 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
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	MacromolecularMachineMixin, 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

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
UNIPROT.ISOFORM	ProteinIsoform
PR	GeneProductMixin MacromolecularComplex Polypeptide Protein ProteinIsoform
ENSEMBL	Gene Transcript Polypeptide Protein ProteinIsoform NoncodingRNAProduct

LinkML Source

name: protein isoform
id_prefixes:
- UniProtKB
- UNIPROT.ISOFORM
- PR
- ENSEMBL
description: Represents a protein that is a specific isoform of the canonical or reference
  protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/
from_schema: https://w3id.org/biolink/biolink-model
aliases:
- proteoform
is_a: protein
mixins:
- gene product isoform mixin