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: http://w3id.org/biolink/vocab/GenomicEntity

Mappings

• SO:0000110
• UMLSSG:GENE

  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 in

• class: MolecularEntity affects expression of GenomicEntity
• class: MolecularEntity affects mutation rate of GenomicEntity
• class: MolecularEntity decreases expression of GenomicEntity
• class: MolecularEntity decreases mutation rate of GenomicEntity
• class: GenomicSequenceLocalization genomic sequence localization.object GenomicEntity
• class: GenomicSequenceLocalization genomic sequence localization.subject GenomicEntity
• class: MolecularEntity increases expression of GenomicEntity
• class: MolecularEntity increases mutation rate of GenomicEntity
• class: SequenceFeatureRelationship sequence feature relationship.object GenomicEntity
• class: SequenceFeatureRelationship sequence feature relationship.subject GenomicEntity

  Fields

• has biological sequence
  • Description: connects a genomic feature to its sequence
  • range: BiologicalSequence
  • Local
• affects abundance of subsets: (translator_minimal)
  • 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
• affects activity of subsets: (translator_minimal)
  • 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
• affects degradation of subsets: (translator_minimal)
  • 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
• affects expression of subsets: (translator_minimal)
  • 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
• affects folding of subsets: (translator_minimal)
  • 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
• affects localization of subsets: (translator_minimal)
  • 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
• affects metabolic processing of subsets: (translator_minimal)
  • 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
• affects molecular modification of subsets: (translator_minimal)
  • 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
• affects mutation rate of subsets: (translator_minimal)
  • 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
• affects response to subsets: (translator_minimal)
  • 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
• affects secretion of subsets: (translator_minimal)
  • 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
• affects splicing of subsets: (translator_minimal)
  • 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
• affects stability of subsets: (translator_minimal)
  • 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
• affects synthesis of subsets: (translator_minimal)
  • 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
• affects transport of subsets: (translator_minimal)
  • 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
• affects uptake of subsets: (translator_minimal)
  • 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
• biomarker for subsets: (translator_minimal)
  • 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
• category subsets: (translator_minimal)
  • 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
• decreases abundance of subsets: (translator_minimal)
  • 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
• decreases activity of subsets: (translator_minimal)
  • 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
• decreases degradation of subsets: (translator_minimal)
  • 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
• decreases expression of subsets: (translator_minimal)
  • 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
• decreases folding of subsets: (translator_minimal)
  • 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
• decreases localization of subsets: (translator_minimal)
  • 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
• decreases metabolic processing of subsets: (translator_minimal)
  • 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
• decreases molecular modification of subsets: (translator_minimal)
  • 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
• decreases mutation rate of subsets: (translator_minimal)
  • 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
• decreases response to subsets: (translator_minimal)
  • 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
• decreases secretion of subsets: (translator_minimal)
  • 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
• decreases splicing of subsets: (translator_minimal)
  • 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
• decreases stability of subsets: (translator_minimal)
  • 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
• decreases synthesis of subsets: (translator_minimal)
  • 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
• decreases transport of subsets: (translator_minimal)
  • 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
• decreases uptake of subsets: (translator_minimal)
  • 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
• description subsets: (translator_minimal)
  • Description: a human-readable description of a thing
  • range: NarrativeText
  • inherited from: NamedThing
• full name
  • Description: a long-form human readable name for a thing
  • range: LabelType
  • inherited from: NamedThing
• has phenotype subsets: (translator_minimal)
  • 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: Phenotype
  • inherited from: BiologicalEntity
• id subsets: (translator_minimal)
  • 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 taxon subsets: (translator_minimal)
  • Description: connects a thing to a class representing a taxon
  • range: OrganismTaxon
  • inherited from: ThingWithTaxon
• increases abundance of subsets: (translator_minimal)
  • 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
• increases activity of subsets: (translator_minimal)
  • 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
• increases degradation of subsets: (translator_minimal)
  • 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
• increases expression of subsets: (translator_minimal)
  • 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
• increases folding of subsets: (translator_minimal)
  • 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
• increases localization of subsets: (translator_minimal)
  • 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
• increases metabolic processing of subsets: (translator_minimal)
  • 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
• increases molecular modification of subsets: (translator_minimal)
  • 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
• increases mutation rate of subsets: (translator_minimal)
  • 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
• increases response to subsets: (translator_minimal)
  • 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
• increases secretion of subsets: (translator_minimal)
  • 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
• increases splicing of subsets: (translator_minimal)
  • 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
• increases stability of subsets: (translator_minimal)
  • 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
• increases synthesis of subsets: (translator_minimal)
  • 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
• increases transport of subsets: (translator_minimal)
  • 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
• increases uptake of subsets: (translator_minimal)
  • 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
• iri subsets: (translator_minimal)
  • Description: An IRI for the node. This is determined by the id using expansion rules.
  • range: IriType
  • inherited from: NamedThing
• molecularly interacts with subsets: (translator_minimal)
  • Description: holds between two entities that make physical contact as part of some interaction
  • range: MolecularEntity
  • inherited from: MolecularEntity
• name subsets: (translator_minimal)
  • Description: A human-readable name for a thing
  • range: LabelType
  • inherited from: NamedThing
• node property
  • Description: A grouping for any property that holds between a node and a value
  • range: string
  • inherited from: NamedThing
• regulates, entity to entity subsets: (translator_minimal)
  • Description: describes an entity that has a direct affect on the state or quality of another existing entity. Use of the ‘affects’ predicate implies that the affected entity already exists, unlike predicates such as ‘affects risk for’ and ‘prevents, where the outcome is something that may or may not come to be.
  • range: MolecularEntity
  • inherited from: MolecularEntity
• related to
  • Description: A grouping for any relationship type that holds between any two things
  • range: NamedThing
  • inherited from: NamedThing
• systematic synonym
  • Description: more commonly used for gene symbols in yeast
  • range: LabelType
  • inherited from: NamedThing