Link

Class: 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

URI: biolink:ChemicalSubstance


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Identifier prefixes

  • PUBCHEM.COMPOUND
  • CHEMBL.COMPOUND
  • UNII
  • CHEBI
  • DRUGBANK
  • MESH
  • CAS
  • DrugCentral
  • GTOPDB
  • HMDB
  • KEGG.COMPOUND
  • ChemBank
  • Aeolus
  • PUBCHEM.SUBSTANCE
  • SIDER.DRUG
  • INCHI
  • INCHIKEY
  • KEGG.GLYCAN
  • KEGG.DRUG
  • KEGG.DGROUP
  • KEGG.ENVIRON

Parents

  • is_a: MolecularEntity - A gene, gene product, small molecule or macromolecule (including protein complex)”

Children

  • Carbohydrate
  • ChemicalExposure - A chemical exposure is an intake of a particular chemical substance, other than a drug.
  • FoodComponent
  • Metabolite - Any intermediate or product resulting from metabolism. Includes primary and secondary metabolites.
  • ProcessedMaterial - A chemical substance (often a mixture) processed for consumption for nutritional, medical or technical use.

Referenced by class

Attributes

Own

  • is metabolite OPT
    • Description: indicates whether a chemical substance is a metabolite
    • range: Boolean

Inherited from entity:

  • id REQ
    • 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 OPT
    • Description: An IRI for an entity. This is determined by the id using expansion rules.
    • range: IriType
    • in subsets: (translator_minimal,samples)
  • 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}
  • type OPT
  • description OPT
    • Description: a human-readable description of an entity
    • range: NarrativeText
    • in subsets: (translator_minimal)
  • source OPT
    • 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 OPT
    • 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

Inherited from named thing:

Inherited from thing with taxon:

  • in taxon 0..*
    • Description: connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see ‘thing with taxon’
    • range: OrganismTaxon
    • in subsets: (translator_minimal)

Domain for slot:

  • is metabolite OPT
    • Description: indicates whether a chemical substance is a metabolite
    • range: Boolean

Other properties

     
In Subsets:   model_organism_database
Exact Mappings:   SIO:010004
    WIKIDATA:Q79529
    UMLSSC:T103
    UMLSST:chem
Narrow Mappings:   UMLSSC:T104
    UMLSST:chvs
    UMLSSC:T109
    UMLSST:orch
    UMLSSC:T114
    UMLSST:nnon
    UMLSSC:T120
    UMLSST:chvf
    UMLSSC:T122
    UMLSST:bodm
    UMLSSC:T130
    UMLSST:irda
    UMLSSC:T131
    UMLSST:hops
    UMLSSC:T196
    UMLSST:elii
    UMLSSC:T197
    UMLSST:inch
Broad Mappings:   UMLSSC:T167
    UMLSST:sbst