Class: SmallMolecule
Description: A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion).
Aliases: chemical substance
classDiagram
class SmallMolecule
MolecularEntity <|-- SmallMolecule
SmallMolecule : available_from
SmallMolecule --|> DrugAvailabilityEnum : available_from
SmallMolecule : category
SmallMolecule : deprecated
SmallMolecule : description
SmallMolecule : full_name
SmallMolecule : has_attribute
SmallMolecule --|> Attribute : has_attribute
SmallMolecule : has_chemical_role
SmallMolecule --|> ChemicalRole : has_chemical_role
SmallMolecule : id
SmallMolecule : iri
SmallMolecule : is_metabolite
SmallMolecule : is_toxic
SmallMolecule : max_tolerated_dose
SmallMolecule : name
SmallMolecule : provided_by
SmallMolecule : synonym
SmallMolecule : trade_name
SmallMolecule : type
SmallMolecule : xref
Inheritance
Slots
| Name | Cardinality and Range | Inheritance | Examples |
|---|---|---|---|
| is_metabolite: indicates whether a molecular entity is a metabolite |
0..1 Boolean |
MolecularEntity | |
| trade_name: |
0..1 String |
ChemicalEntity | |
| available_from: |
* DrugAvailabilityEnum |
ChemicalEntity | |
| 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 |
ChemicalEntity | |
| is_toxic: |
0..1 Boolean |
ChemicalEntity | |
| has_chemical_role: A role is particular behaviour which a chemical entity may exhibit. |
* ChemicalRole |
ChemicalEntity | |
| 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 |
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: small molecule
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 small molecule entity is a molecular entity characterized by availability
in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation
of its precise chemical structure; for convenience of representation, any valid
chemical representation is included, even if it is not strictly molecular (e.g.,
sodium ion).
in_subset:
- model_organism_database
- translator_minimal
from_schema: https://w3id.org/biolink/biolink-model
aliases:
- chemical substance
narrow_mappings:
- STY:T196
- CHEBI:59999
- bioschemas:ChemicalSubstance
- STY:T125
- STY:T197
- STY:T109
- STY:T118
- STY:T111
- STY:T119
- STY:T124
- STY:T115
- STY:T110
- STY:T127
is_a: molecular entity