Class: MolecularEntity
Description: A molecular entity is a chemical entity composed of individual or covalently bonded atoms.
classDiagram
class MolecularEntity
ChemicalEntity <|-- MolecularEntity
MolecularEntity <|-- SmallMolecule
MolecularEntity <|-- NucleicAcidEntity
MolecularEntity : available_from
MolecularEntity --|> DrugAvailabilityEnum : available_from
MolecularEntity : category
MolecularEntity : deprecated
MolecularEntity : description
MolecularEntity : full_name
MolecularEntity : has_attribute
MolecularEntity --|> Attribute : has_attribute
MolecularEntity : has_chemical_role
MolecularEntity --|> ChemicalRole : has_chemical_role
MolecularEntity : id
MolecularEntity : iri
MolecularEntity : is_metabolite
MolecularEntity : is_toxic
MolecularEntity : max_tolerated_dose
MolecularEntity : name
MolecularEntity : provided_by
MolecularEntity : synonym
MolecularEntity : trade_name
MolecularEntity : type
MolecularEntity : xref
Inheritance
Slots
| Name | Cardinality and Range | Inheritance | Examples |
|---|---|---|---|
| is_metabolite: indicates whether a molecular entity is a metabolite |
0..1 Boolean |
direct | |
| 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 |
Usages
| used by | used in | type | used |
|---|---|---|---|
| MolecularEntity | is_metabolite | domain | MolecularEntity |
| SmallMolecule | is_metabolite | domain | MolecularEntity |
| NucleicAcidEntity | is_metabolite | domain | MolecularEntity |
| MolecularActivity | has_input | range | MolecularEntity |
| MolecularActivity | has_output | range | MolecularEntity |
| PairwiseMolecularInteraction | subject | range | MolecularEntity |
| PairwiseMolecularInteraction | object | range | MolecularEntity |
| ReactionToParticipantAssociation | subject | range | MolecularEntity |
| ReactionToCatalystAssociation | subject | range | MolecularEntity |
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: molecular 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 molecular entity is a chemical entity composed of individual or covalently
bonded atoms.
in_subset:
- translator_minimal
from_schema: https://w3id.org/biolink/biolink-model
narrow_mappings:
- STY:T088
- STY:T085
- CHEBI:23367
- bioschemas:MolecularEntity
is_a: chemical entity
slots:
- is metabolite