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

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.

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
    notes:
    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'
    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters
      will be accepted
    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked
      via per-class id slot usage assertions
    - minting authority shoulders should probably be enumerated and checked in the
      pattern
    examples:
    - value: nmdc:mgmag-00-x012.1_7_c1
      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248
    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