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
click ChemicalEntity href "../ChemicalEntity"
OntologyClass <|-- ChemicalEntity
click OntologyClass href "../OntologyClass"
ChemicalEntity : alternative_identifiers
ChemicalEntity : alternative_names
ChemicalEntity : chemical_formula
ChemicalEntity : description
ChemicalEntity : id
ChemicalEntity : inchi
ChemicalEntity : inchi_key
ChemicalEntity : name
ChemicalEntity : smiles
ChemicalEntity : type
Inheritance
- NamedThing
- OntologyClass
- ChemicalEntity
- OntologyClass
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
alternative_names | * String |
A list of alternative names used to refer to the entity | direct |
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 | * String |
A string encoding of a molecular graph, no chiral or isotopic information | direct |
id | 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 | * Uriorcurie |
A list of alternative identifiers for the entity | NamedThing |
type | 1 Uriorcurie |
the class_uri of the class that has been instantiated | NamedThing |
Usages
used by | used in | type | used |
---|---|---|---|
Database | chemical_entity_set | range | ChemicalEntity |
PortionOfSubstance | known_as | range | ChemicalEntity |
MetaboliteIdentification | metabolite_identified | 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:
- alternative_names
- chemical_formula
- inchi
- inchi_key
- smiles
class_uri: nmdc:ChemicalEntity
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:
alternative_names:
name: alternative_names
description: A list of alternative names used to refer to the entity. The distinction
between name and alternative names is application-specific.
from_schema: https://w3id.org/nmdc/nmdc
exact_mappings:
- dcterms:alternative
- skos:altLabel
rank: 1000
alias: alternative_names
owner: ChemicalEntity
domain_of:
- ChemicalEntity
- Study
range: string
multivalued: true
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
alias: smiles
owner: ChemicalEntity
domain_of:
- ChemicalEntity
range: string
multivalued: true
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:
- NamedThing
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:
- PersonValue
- NamedThing
- Protocol
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:
- ImageValue
- NamedThing
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
alias: alternative_identifiers
owner: ChemicalEntity
domain_of:
- MetaboliteIdentification
- NamedThing
range: uriorcurie
multivalued: true
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
type:
name: type
description: the class_uri of the class that has been instantiated
notes:
- replaces legacy nmdc:type slot
- makes it easier to read example data files
- required for polymorphic MongoDB collections
examples:
- value: nmdc:Biosample
- value: nmdc:Study
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://github.com/microbiomedata/nmdc-schema/issues/1048
- https://github.com/microbiomedata/nmdc-schema/issues/1233
- https://github.com/microbiomedata/nmdc-schema/issues/248
rank: 1000
slot_uri: rdf:type
designates_type: true
alias: type
owner: ChemicalEntity
domain_of:
- EukEval
- FunctionalAnnotationAggMember
- MobilePhaseSegment
- PortionOfSubstance
- MagBin
- MetaboliteIdentification
- PeptideQuantification
- ProteinQuantification
- GenomeFeature
- FunctionalAnnotation
- AttributeValue
- NamedThing
- FailureCategorization
- Protocol
- CreditAssociation
- Doi
range: uriorcurie
required: true
class_uri: nmdc:ChemicalEntity