Class: MolecularEntity
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 : description
MolecularEntity : full_name
MolecularEntity : has_attribute
MolecularEntity --|> attribute : has_attribute
MolecularEntity : has_chemical_role
MolecularEntity --|> chemical role : 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 --|> chemical entity : trade_name
MolecularEntity : type
MolecularEntity : xref
Inheritance
Slots
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| is_metabolite | 0..1 Boolean |
indicates whether a molecular entity is a metabolite | direct |
| trade_name | 0..1 ChemicalEntity |
ChemicalEntity | |
| available_from | 0..* DrugAvailabilityEnum |
ChemicalEntity | |
| max_tolerated_dose | 0..1 String |
The highest dose of a drug or treatment that does not cause unacceptable side... | ChemicalEntity |
| is_toxic | 0..1 Boolean |
ChemicalEntity | |
| has_chemical_role | 0..* ChemicalRole |
A role is particular behaviour which a chemical entity may exhibit | ChemicalEntity |
| provided_by | 0..* String |
The value in this node property represents the knowledge provider that create... | NamedThing |
| xref | 0..* Uriorcurie |
A database cross reference or alternative identifier for a NamedThing or edge... | NamedThing |
| full_name | 0..1 LabelType |
a long-form human readable name for a thing | NamedThing |
| synonym | 0..* LabelType |
Alternate human-readable names for a thing | NamedThing |
| id | 1..1 String |
A unique identifier for an entity | Entity |
| iri | 0..1 IriType |
An IRI for an entity | Entity |
| category | 1..* CategoryType |
Name of the high level ontology class in which this entity is categorized | Entity |
| type | 0..* String |
Entity | |
| name | 0..1 LabelType |
A human-readable name for an attribute or entity | Entity |
| description | 0..1 NarrativeText |
a human-readable description of an entity | Entity |
| has_attribute | 0..* Attribute |
connects any entity to an attribute | 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 |
| Exon | is_metabolite | domain | MolecularEntity |
| Transcript | is_metabolite | domain | MolecularEntity |
| CodingSequence | is_metabolite | domain | MolecularEntity |
| RNAProduct | is_metabolite | domain | MolecularEntity |
| RNAProductIsoform | is_metabolite | domain | MolecularEntity |
| NoncodingRNAProduct | is_metabolite | domain | MolecularEntity |
| MicroRNA | is_metabolite | domain | MolecularEntity |
| SiRNA | is_metabolite | domain | MolecularEntity |
| PairwiseMolecularInteraction | subject | range | MolecularEntity |
| PairwiseMolecularInteraction | object | range | MolecularEntity |
| ReactionToParticipantAssociation | subject | range | MolecularEntity |
| ReactionToCatalystAssociation | subject | range | MolecularEntity |
Identifier and Mapping Information
Valid ID Prefixes
Instances of this class should have identifiers with one of the following prefixes:
-
PUBCHEM.COMPOUND
-
CHEMBL.COMPOUND
-
UNII
-
CHEBI
-
DRUGBANK
-
MESH
-
CAS
-
DrugCentral
-
GTOPDB
-
HMDB
-
KEGG.COMPOUND
-
ChemBank
-
PUBCHEM.SUBSTANCE
-
SIDER.DRUG
-
INCHI
-
INCHIKEY
-
KEGG.GLYCAN
-
KEGG.DRUG
-
KEGG.ENVIRON
-
KEGG
-
UMLS
Schema Source
- from schema: https://w3id.org/biolink/biolink-model
Mappings
| Mapping Type | Mapped Value |
|---|---|
| self | biolink:MolecularEntity |
| native | biolink:MolecularEntity |
| narrow | STY:T088, STY:T085, CHEBI:23367, bioschemas:MolecularEntity |
LinkML Source
Direct
name: molecular entity
id_prefixes:
- PUBCHEM.COMPOUND
- CHEMBL.COMPOUND
- UNII
- CHEBI
- DRUGBANK
- MESH
- CAS
- DrugCentral
- GTOPDB
- HMDB
- KEGG.COMPOUND
- ChemBank
- PUBCHEM.SUBSTANCE
- SIDER.DRUG
- INCHI
- INCHIKEY
- 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