Class: ChemicalEntity
An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, drugs. There may be different terms for distinct acid-base forms, protonation states
URI: nmdc:ChemicalEntity
classDiagram
class ChemicalEntity
OntologyClass <|-- ChemicalEntity
ChemicalEntity : alternative_identifiers
ChemicalEntity : chemical_formula
ChemicalEntity : description
ChemicalEntity : id
ChemicalEntity : inchi
ChemicalEntity : inchi_key
ChemicalEntity : name
ChemicalEntity : smiles
Inheritance
- NamedThing
- OntologyClass
- ChemicalEntity
- OntologyClass
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
chemical_formula | 0..1 String |
A generic grouping for molecular formulae and empirical formulae | direct |
inchi | 0..1 String |
direct | |
inchi_key | 0..1 String |
direct | |
smiles | 0..* String |
A string encoding of a molecular graph, no chiral or isotopic information | direct |
id | 1..1 Uriorcurie |
A unique identifier for a thing | NamedThing |
name | 0..1 String |
A human readable label for an entity | NamedThing |
description | 0..1 String |
a human-readable description of a thing | NamedThing |
alternative_identifiers | 0..* Uriorcurie |
A list of alternative identifiers for the entity | NamedThing |
Usages
used by | used in | type | used |
---|---|---|---|
MetaboliteQuantification | metabolite_quantified | range | ChemicalEntity |
ReactionParticipant | chemical | range | ChemicalEntity |
Aliases
- metabolite
- chemical substance
- chemical compound
- chemical
Comments
- As with the parent OntologyClass, we will not assign an nmdc id pattern or typecode to this class.
See Also
Identifier and Mapping Information
Valid ID Prefixes
Instances of this class should have identifiers with one of the following prefixes:
-
cas
-
CHEBI
-
CHEMBL.COMPOUND
-
DRUGBANK
-
HMDB
-
KEGG.COMPOUND
-
MESH
-
PUBCHEM.COMPOUND
Schema Source
- from schema: https://w3id.org/nmdc/nmdc
Mappings
Mapping Type | Mapped Value |
---|---|
self | nmdc:ChemicalEntity |
native | nmdc:ChemicalEntity |
exact | biolink:ChemicalSubstance |
LinkML Source
Direct
name: ChemicalEntity
id_prefixes:
- cas
- CHEBI
- CHEMBL.COMPOUND
- DRUGBANK
- HMDB
- KEGG.COMPOUND
- MESH
- PUBCHEM.COMPOUND
description: An atom or molecule that can be represented with a chemical formula.
Include lipids, glycans, natural products, drugs. There may be different terms for
distinct acid-base forms, protonation states
comments:
- As with the parent OntologyClass, we will not assign an nmdc id pattern or typecode
to this class.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://bioconductor.org/packages/devel/data/annotation/vignettes/metaboliteIDmapping/inst/doc/metaboliteIDmapping.html
aliases:
- metabolite
- chemical substance
- chemical compound
- chemical
exact_mappings:
- biolink:ChemicalSubstance
is_a: OntologyClass
slots:
- chemical_formula
- inchi
- inchi_key
- smiles
Induced
name: ChemicalEntity
id_prefixes:
- cas
- CHEBI
- CHEMBL.COMPOUND
- DRUGBANK
- HMDB
- KEGG.COMPOUND
- MESH
- PUBCHEM.COMPOUND
description: An atom or molecule that can be represented with a chemical formula.
Include lipids, glycans, natural products, drugs. There may be different terms for
distinct acid-base forms, protonation states
comments:
- As with the parent OntologyClass, we will not assign an nmdc id pattern or typecode
to this class.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://bioconductor.org/packages/devel/data/annotation/vignettes/metaboliteIDmapping/inst/doc/metaboliteIDmapping.html
aliases:
- metabolite
- chemical substance
- chemical compound
- chemical
exact_mappings:
- biolink:ChemicalSubstance
is_a: OntologyClass
attributes:
chemical_formula:
name: chemical_formula
description: A generic grouping for molecular formulae and empirical formulae
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: chemical_formula
owner: ChemicalEntity
domain_of:
- ChemicalEntity
range: string
inchi:
name: inchi
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: inchi
owner: ChemicalEntity
domain_of:
- ChemicalEntity
range: string
inchi_key:
name: inchi_key
notes:
- 'key set to false due to rare collisions: Pletnev I, Erin A, McNaught A, Blinov
K, Tchekhovskoi D, Heller S (2012) InChIKey collision resistance: an experimental
testing. J Cheminform. 4:12'
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: inchi_key
owner: ChemicalEntity
domain_of:
- ChemicalEntity
range: string
smiles:
name: smiles
description: A string encoding of a molecular graph, no chiral or isotopic information.
There are usually a large number of valid SMILES which represent a given structure.
For example, CCO, OCC and C(O)C all specify the structure of ethanol.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
multivalued: true
alias: smiles
owner: ChemicalEntity
domain_of:
- ChemicalEntity
range: string
id:
name: id
description: A unique identifier for a thing. Must be either a CURIE shorthand
for a URI or a complete URI
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
identifier: true
alias: id
owner: ChemicalEntity
domain_of:
- Biosample
- Study
- NamedThing
- Activity
range: uriorcurie
required: true
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
name:
name: name
description: A human readable label for an entity
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: name
owner: ChemicalEntity
domain_of:
- Protocol
- NamedThing
- PersonValue
- Activity
range: string
description:
name: description
description: a human-readable description of a thing
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
slot_uri: dcterms:description
alias: description
owner: ChemicalEntity
domain_of:
- Study
- NamedThing
- ImageValue
range: string
alternative_identifiers:
name: alternative_identifiers
description: A list of alternative identifiers for the entity.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
multivalued: true
alias: alternative_identifiers
owner: ChemicalEntity
domain_of:
- Biosample
- Study
- NamedThing
- MetaboliteQuantification
range: uriorcurie
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$