Class: ChemicalEntity

A chemical entity is a physical entity that pertains to chemistry or biochemistry.

URI: biolink:ChemicalEntity

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Identifier prefixes

• UNII
• MESH
• CAS
• UMLS

Parents

• is_a: NamedThing - a databased entity or concept/class

Uses Mixins

• mixin: PhysicalEssence - Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge.
• mixin: ChemicalOrDrugOrTreatment
• mixin: ChemicalEntityOrGeneOrGeneProduct - A union of chemical entities and children, and gene or gene product. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities.
• mixin: ChemicalEntityOrProteinOrPolypeptide - A union of chemical entities and children, and protein and polypeptide. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities.

Children

• ChemicalMixture - A chemical mixture is a chemical entity composed of two or more molecular entities.
• EnvironmentalFoodContaminant
• FoodAdditive
• MolecularEntity - A molecular entity is a chemical entity composed of individual or covalently bonded atoms.
• Nutrient

Referenced by class

• NamedThing associated with resistance to _0..* ChemicalEntity
• NamedThing associated with sensitivity to _0..* ChemicalEntity
• ChemicalToChemicalAssociation chemical to chemical association➞object _1..1 ChemicalEntity
• ChemicalToChemicalDerivationAssociation chemical to chemical derivation association➞object _1..1 ChemicalEntity
• ChemicalToChemicalDerivationAssociation chemical to chemical derivation association➞subject _1..1 ChemicalEntity
• ChemicalEntity chemically interacts with _0..* ChemicalEntity
• ChemicalEntity food component of _0..* ChemicalEntity
• ChemicalEntity has food component _0..* ChemicalEntity
• ChemicalEntity has nutrient _0..* ChemicalEntity
• MolecularActivityToChemicalEntityAssociation molecular activity to chemical entity association➞object _1..1 ChemicalEntity
• NucleicAcidEntity mutation rate decreased by _0..* ChemicalEntity
• NucleicAcidEntity mutation rate increased by _0..* ChemicalEntity
• ChemicalEntity nutrient of _0..* ChemicalEntity
• NamedThing trade name _0..1 ChemicalEntity

Attributes

Own

• available from _0..*
  • Range: drug_availability_enum
• is toxic _0..1
  • Range: Boolean
• max tolerated dose _0..1
  • Description: The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.
  • Range: String
• trade name _0..1
  • Range: ChemicalEntity

Inherited from entity:

• id _1..1
  • 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 _0..1
  • 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 _0..1
  • Range: String
• description _0..1
  • Description: a human-readable description of an entity
  • Range: NarrativeText
  • in subsets: (translator_minimal)
• source _0..1
  • 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 _0..1
  • 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
  • in subsets: (translator_minimal,samples)

Inherited from named thing:

• named thing➞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 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: NamedThing
  • in subsets: (translator_minimal)

Other properties