Link

Class: BiologicalEntity

URI: biolink:BiologicalEntity


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Parents

  • is_a: NamedThing - a databased entity or concept/class

Children

  • BiologicalProcessOrActivity - Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system.
  • DiseaseOrPhenotypicFeature - Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate.
  • EpidemiologicalOutcome - An epidemiological outcome, such as societal disease burden, resulting from an exposure event.
  • Genome - A genome is the sum of genetic material within a cell or virion.
  • GenomicBackgroundExposure - A genomic background exposure is where an individual’s specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of ‘exposure’ to the organism, leading to or influencing an outcome.
  • Genotype - An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background
  • Haplotype - A set of zero or more Alleles on a single instance of a Sequence[VMC]
  • OrganismalEntity - A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities

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 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}
  • 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:

Other properties

     
Aliases:   bioentity
Narrow Mappings:   WIKIDATA:Q28845870
    UMLSSC:T050
    UMLSST:emod
    SIO:010046