Class: molecular entity

A gene, gene product, small molecule or macromolecule (including protein complex)

URI: http://w3id.org/biolink/vocab/MolecularEntity

Mappings

• SIO:010004
• WD:Q43460564

  Inheritance

• is_a: BiologicalEntity
• mixin: ThingWithTaxon - A mixin that can be used on any entity with a taxon

  Children

• ChemicalSubstance - May be a chemical entity or a formulation with a chemical entity as active ingredient, or a complex material with multiple chemical entities as part
• GeneFamily - any grouping of multiple genes or gene products related by common descent
• GenomicEntity - an entity that can either be directly located on a genome (gene, transcript, exon, regulatory region) or is encoded in a genome (protein)

  Used in

• class: MolecularEntity affects abundance of MolecularEntity
• class: MolecularEntity affects activity of MolecularEntity
• class: MolecularEntity affects degradation of MolecularEntity
• class: MolecularEntity affects folding of MolecularEntity
• class: MolecularEntity affects localization of MolecularEntity
• class: MolecularEntity affects metabolic processing of MolecularEntity
• class: MolecularEntity affects molecular modification of MolecularEntity
• class: MolecularEntity affects response to MolecularEntity
• class: MolecularEntity affects secretion of MolecularEntity
• class: MolecularEntity affects stability of MolecularEntity
• class: MolecularEntity affects synthesis of MolecularEntity
• class: MolecularEntity affects transport of MolecularEntity
• class: MolecularEntity affects uptake of MolecularEntity
• class: DiseaseOrPhenotypicFeature correlated with MolecularEntity
• class: MolecularEntity decreases abundance of MolecularEntity
• class: MolecularEntity decreases activity of MolecularEntity
• class: MolecularEntity decreases degradation of MolecularEntity
• class: MolecularEntity decreases folding of MolecularEntity
• class: MolecularEntity decreases localization of MolecularEntity
• class: MolecularEntity decreases metabolic processing of MolecularEntity
• class: MolecularEntity decreases molecular modification of MolecularEntity
• class: MolecularEntity decreases response to MolecularEntity
• class: MolecularEntity decreases secretion of MolecularEntity
• class: MolecularEntity decreases stability of MolecularEntity
• class: MolecularEntity decreases synthesis of MolecularEntity
• class: MolecularEntity decreases transport of MolecularEntity
• class: MolecularEntity decreases uptake of MolecularEntity
• class: GeneToGoTermAssociation gene to go term association.subject MolecularEntity
• class: DiseaseOrPhenotypicFeature has biomarker MolecularEntity
• class: MolecularEntity increases abundance of MolecularEntity
• class: MolecularEntity increases activity of MolecularEntity
• class: MolecularEntity increases degradation of MolecularEntity
• class: MolecularEntity increases folding of MolecularEntity
• class: MolecularEntity increases localization of MolecularEntity
• class: MolecularEntity increases metabolic processing of MolecularEntity
• class: MolecularEntity increases molecular modification of MolecularEntity
• class: MolecularEntity increases response to MolecularEntity
• class: MolecularEntity increases secretion of MolecularEntity
• class: MolecularEntity increases stability of MolecularEntity
• class: MolecularEntity increases synthesis of MolecularEntity
• class: MolecularEntity increases transport of MolecularEntity
• class: MolecularEntity increases uptake of MolecularEntity
• class: MolecularEntity molecularly interacts with MolecularEntity
• class: MolecularEntity negatively regulates, entity to entity MolecularEntity
• class: PairwiseInteractionAssociation pairwise interaction association.object MolecularEntity
• class: PairwiseInteractionAssociation pairwise interaction association.subject MolecularEntity
• class: MolecularEntity positively regulates, entity to entity MolecularEntity
• class: MolecularEntity regulates, entity to entity MolecularEntity

  Fields

• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• 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
  • Local
• molecularly interacts with subsets: (translator_minimal)
  • Description: holds between two entities that make physical contact as part of some interaction
  • range: MolecularEntity
  • Local
• 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
  • Local
• 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
• 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
• iri subsets: (translator_minimal)
  • Description: An IRI for the node. This is determined by the id using expansion rules.
  • range: IriType
  • inherited from: NamedThing
• 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
• 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