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)

SO:0000110

GENO:0000897

UMLSSC:T028

UMLSST:gngm

UMLSSC:T086

UMLSST:nusq

Parents

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.

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
SequenceFeatureRelationship sequence feature relationship➞object _REQ GenomicEntity
SequenceFeatureRelationship sequence feature relationship➞subject _REQ GenomicEntity

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

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)

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}
- range: CategoryType
- in subsets: (translator_minimal)

in taxon _0..*
- Description: connects a thing to a class representing a taxon
- range: OrganismTaxon
- in subsets: (translator_minimal)