Class: genomic entity

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

Inheritance

• 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
• 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.
• 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

  Used by

• 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
• 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

  Fields

• affects abundance of _0..*
  • Description: holds between two molecular entities where the action or effect of one changes the amount of the other within a system of interest
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• affects activity of _0..*
  • Description: holds between two molecular entities where the action or effect of one changes the activity of the other within a system of interest
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• affects degradation of _0..*
  • Description: holds between two molecular entities where the action or effect of one impacts the rate of degradation of the other within a system of interest
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• affects expression of _0..*
  • Description: holds between two molecular entities where the action or effect of one changes the level of expression of the other within a system of interest
  • range: GenomicEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• affects folding of _0..*
  • Description: holds between two molecular entities where the action or effect of one changes the rate or quality of folding of the other
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• affects localization of _0..*
  • Description: holds between two molecular entities where the action or effect of one changes the localization of the other within a system of interest
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• affects metabolic processing of _0..*
  • Description: holds between two molecular entities where the action or effect of one impacts the metabolic processing of the other within a system of interest
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• affects molecular modification of _0..*
  • Description: holds between two molecular entities where the action or effect of one leads changes in the molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• affects mutation rate of _0..*
  • Description: holds between a molecular entity and a genomic entity where the action or effect of the molecular entity impacts the rate of mutation of the genomic entity within a system of interest
  • range: GenomicEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• affects response to _0..*
  • Description: holds between two molecular entities where the action or effect of one impacts the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine, biological or pathological process) to the other
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• affects secretion of _0..*
  • Description: holds between two molecular entities where the action or effect of one impacts the rate of secretion of the other out of a cell, gland, or organ
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• affects splicing of _0..*
  • Description: holds between a molecular entity and an mRNA where the action or effect of the molecular entity impacts the splicing of the mRNA
  • range: Transcript
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• affects stability of _0..*
  • Description: holds between two molecular entities where the action or effect of one impacts the stability of the other within a system of interest
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• affects synthesis of _0..*
  • Description: holds between two molecular entities where the action or effect of one impacts the rate of chemical synthesis of the other
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• affects transport of _0..*
  • Description: holds between two molecular entities where the action or effect of one impacts the rate of transport of the other across some boundary in a system of interest
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• affects uptake of _0..*
  • Description: holds between two molecular entities where the action or effect of one impacts the rate of uptake of the other into of a cell, gland, or organ
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• biomarker for _0..*
  • Description: holds between a measurable molecular entity and a disease or phenotypic feature, where the entity is used as an indicator of the presence or state of the disease or feature.
  • range: DiseaseOrPhenotypicFeature
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• 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
  • range: IriType
  • inherited from: NamedThing
  • in subsets: (translator_minimal)
• decreases abundance of _0..*
  • Description: holds between two molecular entities where the action or effect of one decreases the amount of the other within a system of interest
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• decreases activity of _0..*
  • Description: holds between two molecular entities where the action or effect of one decreases the activity of the other within a system of interest
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• decreases degradation of _0..*
  • Description: holds between two molecular entities where the action or effect of one decreases the rate of degradation of the other within a system of interest
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• decreases expression of _0..*
  • Description: holds between two molecular entities where the action or effect of one decreases the level of expression of the other within a system of interest
  • range: GenomicEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• decreases folding of _0..*
  • Description: holds between two molecular entities where the action or effect of one decreases the rate or quality of folding of the other
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• decreases localization of _0..*
  • Description: holds between two molecular entities where the action or effect of one decreases the proper localization of the other within a system of interest
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• decreases metabolic processing of _0..*
  • Description: holds between two molecular entities where the action or effect of one decreases the rate of metabolic processing of the other within a system of interest
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• decreases molecular modification of _0..*
  • Description: holds between two molecular entities where the action or effect of one leads to decreased molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• decreases mutation rate of _0..*
  • Description: holds between a molecular entity and a genomic entity where the action or effect of the molecular entity decreases the rate of mutation of the genomic entity within a system of interest
  • range: GenomicEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• decreases response to _0..*
  • Description: holds between two molecular entities where the action or effect of one decreases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine, biological or pathological process) to the other
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• decreases secretion of _0..*
  • Description: holds between two molecular entities where the action or effect of one decreases the rate of secretion of the other out of a cell, gland, or organ
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• decreases splicing of _0..*
  • Description: holds between a molecular entity and an mRNA where the action or effect of the molecular entity decreases the proper splicing of the mRNA
  • range: Transcript
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• decreases stability of _0..*
  • Description: holds between two molecular entities where the action or effect of one decreases the stability of the other within a system of interest
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• decreases synthesis of _0..*
  • Description: holds between two molecular entities where the action or effect of one decreases the rate of chemical synthesis of the other
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• decreases transport of _0..*
  • Description: holds between two molecular entities where the action or effect of one decreases the rate of transport of the other across some boundary in a system of interest
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• decreases uptake of _0..*
  • Description: holds between two molecular entities where the action or effect of one decreases the rate of uptake of the other into of a cell, gland, or organ
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• description _OPT
  • Description: a human-readable description of a thing
  • range: NarrativeText
  • inherited from: NamedThing
  • in subsets: (translator_minimal)
• full name _OPT
  • Description: a long-form human readable name for a thing
  • range: LabelType
  • inherited from: NamedThing
• has biological sequence _OPT
  • Description: connects a genomic feature to its sequence
  • range: BiologicalSequence
• has phenotype _0..*
  • Description: holds between a biological entity and a phenotype, where a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature).
  • range: PhenotypicFeature
  • inherited from: BiologicalEntity
  • in subsets: (translator_minimal)
• id _REQ
  • Description: A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI
  • range: IdentifierType
  • inherited from: NamedThing
  • in subsets: (translator_minimal)
• in taxon _0..*
  • Description: connects a thing to a class representing a taxon
  • range: OrganismTaxon
  • inherited from: ThingWithTaxon
  • in subsets: (translator_minimal)
• increases abundance of _0..*
  • Description: holds between two molecular entities where the action or effect of one increases the amount of the other within a system of interest
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• increases activity of _0..*
  • Description: holds between two molecular entities where the action or effect of one increases the activity of the other within a system of interest
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• increases degradation of _0..*
  • Description: holds between two molecular entities where the action or effect of one increases the rate of degradation of the other within a system of interest
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• increases expression of _0..*
  • Description: holds between two molecular entities where the action or effect of one increases the level of expression of the other within a system of interest
  • range: GenomicEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• increases folding of _0..*
  • Description: holds between two molecular entities where the action or effect of one increases the rate or quality of folding of the other
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• increases localization of _0..*
  • Description: holds between two molecular entities where the action or effect of one increases the proper localization of the other within a system of interest
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• increases metabolic processing of _0..*
  • Description: holds between two molecular entities where the action or effect of one increases the rate of metabolic processing of the other within a system of interest
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• increases molecular modification of _0..*
  • Description: holds between two molecular entities where the action or effect of one leads to increased molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• increases mutation rate of _0..*
  • Description: holds between a molecular entity and a genomic entity where the action or effect of the molecular entity increases the rate of mutation of the genomic entity within a system of interest
  • range: GenomicEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• increases response to _0..*
  • Description: holds between two molecular entities where the action or effect of one increases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine, biological or pathological process) to the other
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• increases secretion of _0..*
  • Description: holds between two molecular entities where the action or effect of one increases the rate of secretion of the other out of a cell, gland, or organ
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• increases splicing of _0..*
  • Description: holds between a molecular entity and an mRNA where the action or effect of the molecular entity increases the proper splicing of the mRNA
  • range: Transcript
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• increases stability of _0..*
  • Description: holds between two molecular entities where the action or effect of one increases the stability of the other within a system of interest
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• increases synthesis of _0..*
  • Description: holds between two molecular entities where the action or effect of one increases the rate of chemical synthesis of the other
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• increases transport of _0..*
  • Description: holds between two molecular entities where the action or effect of one increases the rate of transport of the other across some boundary in a system of interest
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• increases uptake of _0..*
  • Description: holds between two molecular entities where the action or effect of one increases the rate of uptake of the other into of a cell, gland, or organ
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• interacts with _0..*
  • Description: holds between any two entities that directly or indirectly interact with each other
  • range: NamedThing
  • inherited from: NamedThing
  • in subsets: (translator_minimal)
• iri _OPT
  • Description: An IRI for the node. This is determined by the id using expansion rules.
  • range: IriType
  • inherited from: NamedThing
  • in subsets: (translator_minimal)
• molecularly interacts with _0..*
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• name _OPT
  • Description: A human-readable name for a thing
  • range: LabelType
  • inherited from: NamedThing
  • in subsets: (translator_minimal)
• node property _OPT
  • Description: A grouping for any property that holds between a node and a value
  • range: String
  • inherited from: NamedThing
• regulates, entity to entity _0..*
  • range: MolecularEntity
  • inherited from: MolecularEntity
  • in subsets: (translator_minimal)
• related to _0..*
  • Description: A relationship that is asserted between two named things
  • range: NamedThing
  • inherited from: NamedThing
• synonym _0..*
  • Description: Alternate human-readable names for a thing
  • range: LabelType
  • inherited from: NamedThing
  • in subsets: (translator_minimal)
• systematic synonym _OPT
  • Description: more commonly used for gene symbols in yeast
  • range: LabelType
  • inherited from: NamedThing