Link

Class: MolecularEntity

A gene, gene product, small molecule or macromolecule (including protein complex)”

URI: biolink:MolecularEntity


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Parents

Uses Mixins

  • mixin: ThingWithTaxon - A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes
  • mixin: PhysicalEssence - Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge.

Children

  • ChemicalSubstance - May be a chemical entity or a formulation with a chemical entity as active ingredient, or a complex material with multiple chemical entities as part
  • Drug - A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease
  • Food - A substance consumed by a living organism as a source of nutrition
  • GeneFamily - any grouping of multiple genes or gene products related by common descent
  • GenomicEntity - an entity that can either be directly located on a genome (gene, transcript, exon, regulatory region) or is encoded in a genome (protein)

Referenced by class

Attributes

Inherited from entity:

  • id REQ
    • 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 OPT
    • Description: An IRI for an entity. This is determined by the id using expansion rules.
    • range: IriType
    • in subsets: (translator_minimal,samples)
  • category 1..*
    • 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 bl:Protein, bl:GeneProduct, bl: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 {bl:GenomicEntity, bl:MolecularEntity, bl:NamedThing}
  • type OPT
  • description OPT
    • Description: a human-readable description of an entity
    • range: NarrativeText
    • in subsets: (translator_minimal)
  • source OPT
    • Description: a lightweight analog to the association class ‘has provider’ slot, which is the string name, or the authoritative (i.e. database) namespace, designating the origin of the entity to which the slot belongs.
    • range: LabelType
    • in subsets: (translator_minimal)
  • provided by 0..*
    • Description: connects an association to the agent (person, organization or group) that provided it
    • range: Agent
  • has attribute 0..*
    • Description: connects any entity to an attribute
    • range: Attribute
    • in subsets: (samples)

Inherited from macromolecular machine mixin:

  • macromolecular machine mixin➞name OPT
    • Description: 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
    • range: SymbolType

Inherited from named thing:

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)

Other properties

     
Aliases:   bioentity
Exact Mappings:   CHEBI:24431
Narrow Mappings:   SIO:010341
    WIKIDATA:Q43460564
    UMLSSG:CHEM
    UMLSSC:T085
    UMLSST:mosq
    UMLSSC:T123
    UMLSST:bacs
    UMLSSC:T125
    UMLSST:horm
    UMLSSC:T126
    UMLSST:enzy
    UMLSSC:T129
    UMLSST:imft
    UMLSSC:T192
    UMLSST:rcpt