Class: ChemicalEntity (DEPRECATED)

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. A chemical entity is a physical entity that pertains to chemistry or biochemistry.

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 : definition ChemicalEntity : description ChemicalEntity : id ChemicalEntity : name ChemicalEntity : relations ChemicalEntity --> "*" OntologyRelation : relations click OntologyRelation href "../OntologyRelation" ChemicalEntity : type

Inheritance

NamedThing
- OntologyClass
  - ChemicalEntity

Slots

Name	Cardinality and Range	Description	Inheritance
chemical_formula	0..1 String	A generic grouping for molecular formulae and empirical formulae	direct
alternative_names	* String	A list of alternative names used to refer to the entity	OntologyClass
definition	0..1 String	The definition of the ontology term as provided by the ontology	OntologyClass
relations	* OntologyRelation		OntologyClass
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

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:

CHEBI
MS

Schema Source

from schema: https://w3id.org/nmdc/nmdc

Mappings

Mapping Type	Mapped Value
exact	biolink:ChemicalSubstance

LinkML Source

Direct

name: ChemicalEntity
id_prefixes:
- CHEBI
- MS
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. A chemical entity is a  physical entity
  that pertains to chemistry or biochemistry.
deprecated: true; as of Jan 2025, NMDC only needs a handful of chemicals and its use
  cases can be served via an enumeration rather than supporting a full class.
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
class_uri: nmdc:ChemicalEntity

Induced

name: ChemicalEntity
id_prefixes:
- CHEBI
- MS
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. A chemical entity is a  physical entity
  that pertains to chemistry or biochemistry.
deprecated: true; as of Jan 2025, NMDC only needs a handful of chemicals and its use
  cases can be served via an enumeration rather than supporting a full class.
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
  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:
    - OntologyClass
    - Study
    range: string
    multivalued: true
  definition:
    name: definition
    description: The definition of the ontology term as provided by the ontology.
    from_schema: https://w3id.org/nmdc/basic_classes
    rank: 1000
    alias: definition
    owner: ChemicalEntity
    domain_of:
    - OntologyClass
    range: string
  relations:
    name: relations
    from_schema: https://w3id.org/nmdc/basic_classes
    rank: 1000
    alias: relations
    owner: ChemicalEntity
    domain_of:
    - OntologyClass
    range: OntologyRelation
    multivalued: true
    inlined: true
    inlined_as_list: 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:
    - The identifiers for terms from external ontologies can't have their ids constrained
      to the nmdc namespace
    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
    structured_aliases:
      workflow_execution_id:
        literal_form: workflow_execution_id
        predicate: NARROW_SYNONYM
        contexts:
        - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
      data_object_id:
        literal_form: data_object_id
        predicate: NARROW_SYNONYM
        contexts:
        - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
    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
    structured_aliases:
      workflow_execution_class:
        literal_form: workflow_execution_class
        predicate: NARROW_SYNONYM
        contexts:
        - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
    rank: 1000
    slot_uri: rdf:type
    designates_type: true
    alias: type
    owner: ChemicalEntity
    domain_of:
    - EukEval
    - FunctionalAnnotationAggMember
    - PeptideQuantification
    - ProteinQuantification
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - OntologyRelation
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    range: uriorcurie
    required: true
class_uri: nmdc:ChemicalEntity