Class: ChemicalEntity
Description: A chemical entity is a physical entity that pertains to chemistry or biochemistry.
classDiagram
class ChemicalEntity
PhysicalEssence <|-- ChemicalEntity
ChemicalOrDrugOrTreatment <|-- ChemicalEntity
ChemicalEntityOrGeneOrGeneProduct <|-- ChemicalEntity
ChemicalEntityOrProteinOrPolypeptide <|-- ChemicalEntity
NamedThing <|-- ChemicalEntity
ChemicalEntity <|-- MolecularEntity
ChemicalEntity <|-- ChemicalMixture
ChemicalEntity <|-- EnvironmentalFoodContaminant
ChemicalEntity <|-- FoodAdditive
ChemicalEntity : available_from
ChemicalEntity --|> DrugAvailabilityEnum : available_from
ChemicalEntity : category
ChemicalEntity : deprecated
ChemicalEntity : description
ChemicalEntity : full_name
ChemicalEntity : has_attribute
ChemicalEntity --|> Attribute : has_attribute
ChemicalEntity : has_chemical_role
ChemicalEntity --|> ChemicalRole : has_chemical_role
ChemicalEntity : id
ChemicalEntity : iri
ChemicalEntity : is_toxic
ChemicalEntity : max_tolerated_dose
ChemicalEntity : name
ChemicalEntity : provided_by
ChemicalEntity : synonym
ChemicalEntity : trade_name
ChemicalEntity : type
ChemicalEntity : xref
Inheritance
Slots
| Name | Cardinality and Range | Inheritance | Examples |
|---|---|---|---|
| trade_name: |
0..1 String |
direct | |
| available_from: |
* DrugAvailabilityEnum |
direct | |
| max_tolerated_dose: 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. |
0..1 String |
direct | |
| is_toxic: |
0..1 Boolean |
direct | |
| has_chemical_role: A role is particular behaviour which a chemical entity may exhibit. |
* ChemicalRole |
direct | |
| provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph. |
* String |
NamedThing | |
| xref: A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references. |
* Uriorcurie |
NamedThing | |
| full_name: a long-form human readable name for a thing |
0..1 LabelType |
NamedThing | |
| synonym: Alternate human-readable names for a thing |
* LabelType |
NamedThing | |
| id: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI |
1 String |
Entity | |
| iri: An IRI for an entity. This is determined by the id using expansion rules. |
0..1 IriType |
Entity | |
| category: 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} |
1..* Uriorcurie |
Entity | |
| type: None |
* String |
Entity | |
| name: A human-readable name for an attribute or entity. |
0..1 LabelType |
Entity | |
| description: a human-readable description of an entity |
0..1 NarrativeText |
Entity | |
| has_attribute: connects any entity to an attribute |
* Attribute |
Entity | |
| deprecated: A boolean flag indicating that an entity is no longer considered current or valid. |
0..1 Boolean |
Entity |
Usages
Valid ID Prefixes
Instances of this class should have identifiers with one of the following prefixes, ordered with the most preferred first:
LinkML Source
name: chemical entity
id_prefixes:
- CHEBI
- UNII
- PUBCHEM.COMPOUND
- CHEMBL.COMPOUND
- DRUGBANK
- MESH
- CAS
- DrugCentral
- GTOPDB
- HMDB
- KEGG.COMPOUND
- PHARMGKB.DRUG
- ChemBank
- PUBCHEM.SUBSTANCE
- SIDER.DRUG
- INCHI
- INCHIKEY
- BIGG.METABOLITE
- foodb.compound
- KEGG.GLYCAN
- KEGG.DRUG
- KEGG.ENVIRON
- KEGG
- UMLS
description: A chemical entity is a physical entity that pertains to chemistry or
biochemistry.
in_subset:
- translator_minimal
from_schema: https://w3id.org/biolink/biolink-model
exact_mappings:
- CHEBI:24431
- SIO:010004
- WIKIDATA:Q79529
- STY:T103
narrow_mappings:
- WIKIDATA:Q43460564
- STY:T123
- STY:T131
broad_mappings:
- STY:T167
is_a: named thing
mixins:
- physical essence
- chemical or drug or treatment
- chemical entity or gene or gene product
- chemical entity or protein or polypeptide
slots:
- trade name
- available from
- max tolerated dose
- is toxic
- has chemical role