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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

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

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_\-\/\.,]*$