Class: GenomicEntity

an entity that can either be directly located on a genome (gene, transcript, exon, regulatory region) or is encoded in a genome (protein)

URI: biolink:GenomicEntity









  • is_a: MolecularEntity - A gene, gene product, small molecule or macromolecule (including protein complex)


  • CodingSequence
  • Exon - A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing
  • Genome - A genome is the sum of genetic material within a cell or virion.
  • Genotype - An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some extablished background
  • Haplotype - A set of zero or more Alleles on a single instance of a Sequence[VMC]
  • MacromolecularMachine - A union of gene, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this.
  • ReagentTargetedGene - A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi
  • SequenceVariant - An allele that varies in its sequence from what is considered the reference allele at that locus.

Referenced by class



Inherited from gene product:

  • id REQ
    • Description: A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI
    • range: String
    • in subsets: (translator_minimal)
  • name REQ
    • Description: A human-readable name for a thing
    • range: LabelType
    • in subsets: (translator_minimal)

Inherited from named thing:

  • 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}

Inherited from thing with taxon:

  • in taxon 0..*
    • Description: connects a thing to a class representing a taxon
    • range: OrganismTaxon
    • in subsets: (translator_minimal)

Other properties

Aliases:   sequence feature
Mappings:   SO:0000110