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

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Parents

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

Children

• CodingSequence
• Exon - A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.
• Gene - A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions.
• 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]
• Protein - A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA
• 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.
• Transcript - An RNA synthesized on a DNA or RNA template by an RNA polymerase.

Referenced by class

• MolecularEntity affects expression of _0..* GenomicEntity
• MolecularEntity affects mutation rate of _0..* GenomicEntity
• MolecularEntity decreases expression of _0..* GenomicEntity
• MolecularEntity decreases mutation rate of _0..* GenomicEntity
• GenomicSequenceLocalization genomic sequence localization➞object _REQ GenomicEntity
• GenomicSequenceLocalization genomic sequence localization➞subject _REQ GenomicEntity
• GenomicEntity has sequence location _0..* GenomicEntity
• MolecularEntity increases expression of _0..* GenomicEntity
• MolecularEntity increases mutation rate of _0..* GenomicEntity
• SequenceVariant is sequence variant of _0..* GenomicEntity
• SequenceFeatureRelationship sequence feature relationship➞object _REQ GenomicEntity
• SequenceFeatureRelationship sequence feature relationship➞subject _REQ GenomicEntity

Attributes

Own

• has biological sequence _OPT
  • Description: connects a genomic feature to its sequence
  • range: BiologicalSequence

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}
  • range: CategoryType
  • in subsets: (translator_minimal)
• type _OPT
  • range: String
• 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:

• named thing➞category _1..*
  • range: NamedThing

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