Class: ChemicalEntity

Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.

URI: CHEBI:23367

classDiagram class ChemicalEntity click ChemicalEntity href "../ChemicalEntity/" MaterialEntity <|-- ChemicalEntity click MaterialEntity href "../MaterialEntity/" ChemicalEntity <|-- ShiftCalibrationCompound click ShiftCalibrationCompound href "../ShiftCalibrationCompound/" ChemicalEntity <|-- CharacterizedCompound click CharacterizedCompound href "../CharacterizedCompound/" ChemicalEntity <|-- Atom click Atom href "../Atom/" ChemicalEntity : alternative_label ChemicalEntity : description ChemicalEntity : has_density ChemicalEntity --> "* _recommended_" Density : has_density click Density href "../Density/" ChemicalEntity : has_mass ChemicalEntity --> "* _recommended_" Mass : has_mass click Mass href "../Mass/" ChemicalEntity : has_molar_mass ChemicalEntity --> "* _recommended_" MolarMass : has_molar_mass click MolarMass href "../MolarMass/" ChemicalEntity : has_part ChemicalEntity --> "* _recommended_" MaterialEntity : has_part click MaterialEntity href "../MaterialEntity/" ChemicalEntity : has_physical_state ChemicalEntity --> "0..1" PhysicalStateEnum : has_physical_state click PhysicalStateEnum href "../PhysicalStateEnum/" ChemicalEntity : has_pressure ChemicalEntity --> "* _recommended_" Pressure : has_pressure click Pressure href "../Pressure/" ChemicalEntity : has_qualitative_attribute ChemicalEntity --> "* _recommended_" QualitativeAttribute : has_qualitative_attribute click QualitativeAttribute href "../QualitativeAttribute/" ChemicalEntity : has_quantitative_attribute ChemicalEntity --> "* _recommended_" QuantitativeAttribute : has_quantitative_attribute click QuantitativeAttribute href "../QuantitativeAttribute/" ChemicalEntity : has_temperature ChemicalEntity --> "* _recommended_" Temperature : has_temperature click Temperature href "../Temperature/" ChemicalEntity : has_volume ChemicalEntity --> "* _recommended_" Volume : has_volume click Volume href "../Volume/" ChemicalEntity : id ChemicalEntity : inchi ChemicalEntity --> "* _recommended_" InChi : inchi click InChi href "../InChi/" ChemicalEntity : inchikey ChemicalEntity --> "* _recommended_" InChIKey : inchikey click InChIKey href "../InChIKey/" ChemicalEntity : iupac_name ChemicalEntity --> "* _recommended_" IUPACName : iupac_name click IUPACName href "../IUPACName/" ChemicalEntity : molecular_formula ChemicalEntity --> "* _recommended_" MolecularFormula : molecular_formula click MolecularFormula href "../MolecularFormula/" ChemicalEntity : other_identifier ChemicalEntity --> "*" Identifier : other_identifier click Identifier href "../Identifier/" ChemicalEntity : part_of ChemicalEntity --> "*" Entity : part_of click Entity href "../Entity/" ChemicalEntity : rdf_type ChemicalEntity --> "0..1 _recommended_" DefinedTerm : rdf_type click DefinedTerm href "../DefinedTerm/" ChemicalEntity : smiles ChemicalEntity --> "* _recommended_" SMILES : smiles click SMILES href "../SMILES/" ChemicalEntity : title ChemicalEntity : type ChemicalEntity --> "0..1" DefinedTerm : type click DefinedTerm href "../DefinedTerm/"

Inheritance

Entity [ ClassifierMixin]
- MaterialEntity [ Materialistic]
  - ChemicalEntity

Slots

Name	Cardinality and Range	Description	Inheritance
inchi	* recommended InChi	The slot to provide the InChi descriptor of a ChemicalEntity	direct
inchikey	* recommended InChIKey	The slot to provide the InChiKey of a ChemicalEntity	direct
smiles	* recommended SMILES	The slot to provide the canonical SMILES descriptor of a ChemicalEntity	direct
molecular_formula	* recommended MolecularFormula	The slot to provide the IUPAC formula of a ChemicalEntity	direct
iupac_name	* recommended IUPACName	The slot to provide the IUPAC name of a ChemicalEntity	direct
has_molar_mass	* recommended MolarMass	The slot to provide the MolarMass of a ChemicalEntity	direct
alternative_label	0..1 String	The slot to specify an alternative label, name or title for a MaterialEntity	Materialistic
has_physical_state	0..1 PhysicalStateEnum	The slot to specify the physical state of a MaterialEntity	Materialistic
has_temperature	* recommended Temperature	The slot to provide the Temperature of a MaterialEntity	Materialistic
has_mass	* recommended Mass	The slot to provide the Mass of a MaterialEntity	Materialistic
has_volume	* recommended Volume	The slot to provide the Volume of a MaterialEntity	Materialistic
has_density	* recommended Density	The slot to provide the Density of a MaterialEntity	Materialistic
has_pressure	* recommended Pressure	The slot to provide the Pressure of a MaterialEntity	Materialistic
title	0..1 String	The slot to provide a title for the Entity	Entity
description	0..1 String	The slot to provide a description for the Entity	Entity
id	1 Uriorcurie	A slot to provide an URI for an entity within this schema	Entity
other_identifier	* Identifier	A slot to provide a secondary identifier of the Entity	Entity
has_qualitative_attribute	* recommended QualitativeAttribute	The slot to relate a qualitative attribute to an EvaluatedEntity, EvaluatedAc...	Entity
has_quantitative_attribute	* recommended QuantitativeAttribute	The slot to relate a quantitative attribute to an EvaluatedEntity, EvaluatedA...	Entity
has_part	* recommended MaterialEntity	The slot to provide the parts of a MaterialEntity	Entity
part_of	* Entity	The slot to specify an Entity of which the Entity is a part	Entity
type	0..1 DefinedTerm	This slot is described in more detail within the class in which it is used	ClassifierMixin
rdf_type	0..1 recommended DefinedTerm	The slot to specify the ontology class that is instantiated by an entity	ClassifierMixin

Usages

used by	used in	type	used
NMRSolvent	composed_of	range	ChemicalEntity
ChemicalSubstance	composed_of	range	ChemicalEntity
Polymer	composed_of	range	ChemicalEntity
StartingMaterial	composed_of	range	ChemicalEntity
DissolvingSubstance	composed_of	range	ChemicalEntity
Reagent	composed_of	range	ChemicalEntity
ChemicalProduct	composed_of	range	ChemicalEntity
Catalyst	composed_of	range	ChemicalEntity
SubstanceSample	composed_of	range	ChemicalEntity
PolymerSample	composed_of	range	ChemicalEntity

Identifier and Mapping Information

Schema Source

from schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml

Mappings

Mapping Type	Mapped Value
self	CHEBI:23367
native	nmr_dcat_ap:ChemicalEntity

LinkML Source

Direct

name: ChemicalEntity
description: Any constitutionally or isotopically distinct atom, molecule, ion, ion
  pair, radical, radical ion, complex, conformer etc., identifiable as a separately
  distinguishable entity.
from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
is_a: MaterialEntity
slots:
- inchi
- inchikey
- smiles
- molecular_formula
- iupac_name
- has_molar_mass
class_uri: CHEBI:23367

Induced

name: ChemicalEntity
description: Any constitutionally or isotopically distinct atom, molecule, ion, ion
  pair, radical, radical ion, complex, conformer etc., identifiable as a separately
  distinguishable entity.
from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
is_a: MaterialEntity
attributes:
  inchi:
    name: inchi
    description: The slot to provide the InChi descriptor of a ChemicalEntity.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    is_a: has_qualitative_attribute
    slot_uri: SIO:000008
    alias: inchi
    owner: ChemicalEntity
    domain_of:
    - ChemicalEntity
    range: InChi
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  inchikey:
    name: inchikey
    description: The slot to provide the InChiKey of a ChemicalEntity.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    is_a: has_qualitative_attribute
    slot_uri: SIO:000008
    alias: inchikey
    owner: ChemicalEntity
    domain_of:
    - ChemicalEntity
    range: InChIKey
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  smiles:
    name: smiles
    description: The slot to provide the canonical SMILES descriptor of a ChemicalEntity.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    is_a: has_qualitative_attribute
    slot_uri: SIO:000008
    alias: smiles
    owner: ChemicalEntity
    domain_of:
    - ChemicalEntity
    range: SMILES
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  molecular_formula:
    name: molecular_formula
    description: The slot to provide the IUPAC formula of a ChemicalEntity.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    is_a: has_qualitative_attribute
    slot_uri: SIO:000008
    alias: molecular_formula
    owner: ChemicalEntity
    domain_of:
    - ChemicalEntity
    range: MolecularFormula
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  iupac_name:
    name: iupac_name
    description: The slot to provide the IUPAC name of a ChemicalEntity.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    is_a: has_qualitative_attribute
    slot_uri: SIO:000008
    alias: iupac_name
    owner: ChemicalEntity
    domain_of:
    - ChemicalEntity
    range: IUPACName
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_molar_mass:
    name: has_molar_mass
    description: The slot to provide the MolarMass of a ChemicalEntity.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    is_a: has_mass
    slot_uri: SIO:000008
    alias: has_molar_mass
    owner: ChemicalEntity
    domain_of:
    - ChemicalEntity
    range: MolarMass
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  alternative_label:
    name: alternative_label
    description: The slot to specify an alternative label, name or title for a MaterialEntity.
    todos:
    - Should probably rather declared on Entity or in some common metadata mixin instead.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    slot_uri: skos:altLabel
    alias: alternative_label
    owner: ChemicalEntity
    domain_of:
    - Materialistic
    range: string
  has_physical_state:
    name: has_physical_state
    description: The slot to specify the physical state of a MaterialEntity.
    todos:
    - Find out how to make this a subproperty of has_qualitative_attribute, as it
      currently throws the error 'physical_state enumerations cannot be inlined' due
      to the fact that we are using an enum here.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    slot_uri: SIO:000008
    alias: has_physical_state
    owner: ChemicalEntity
    domain_of:
    - Materialistic
    range: PhysicalStateEnum
    multivalued: false
    inlined: false
  has_temperature:
    name: has_temperature
    description: The slot to provide the Temperature of a MaterialEntity.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    is_a: has_quantitative_attribute
    slot_uri: SIO:000008
    alias: has_temperature
    owner: ChemicalEntity
    domain_of:
    - Materialistic
    - ChemicalReaction
    range: Temperature
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_mass:
    name: has_mass
    description: The slot to provide the Mass of a MaterialEntity.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    is_a: has_quantitative_attribute
    slot_uri: SIO:000008
    alias: has_mass
    owner: ChemicalEntity
    domain_of:
    - Materialistic
    range: Mass
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_volume:
    name: has_volume
    description: The slot to provide the Volume of a MaterialEntity.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    is_a: has_quantitative_attribute
    slot_uri: SIO:000008
    alias: has_volume
    owner: ChemicalEntity
    domain_of:
    - Materialistic
    range: Volume
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_density:
    name: has_density
    description: The slot to provide the Density of a MaterialEntity.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    is_a: has_quantitative_attribute
    slot_uri: SIO:000008
    alias: has_density
    owner: ChemicalEntity
    domain_of:
    - Materialistic
    range: Density
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_pressure:
    name: has_pressure
    description: The slot to provide the Pressure of a MaterialEntity.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    is_a: has_quantitative_attribute
    slot_uri: SIO:000008
    alias: has_pressure
    owner: ChemicalEntity
    domain_of:
    - Materialistic
    - ChemicalReaction
    range: Pressure
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  title:
    name: title
    description: The slot to provide a title for the Entity.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    slot_uri: dcterms:title
    alias: title
    owner: ChemicalEntity
    domain_of:
    - Activity
    - AgenticEntity
    - Any
    - Attribution
    - Catalogue
    - CatalogueRecord
    - ChecksumAlgorithm
    - Concept
    - ConceptScheme
    - DataService
    - Dataset
    - DatasetSeries
    - DefinedTerm
    - Distribution
    - Document
    - Entity
    - Frequency
    - Geometry
    - Identifier
    - LegalResource
    - LicenseDocument
    - LinguisticSystem
    - MediaType
    - MediaTypeOrExtent
    - PeriodOfTime
    - Plan
    - Policy
    - ProvenanceStatement
    - QualitativeAttribute
    - QuantitativeAttribute
    - Resource
    - RightsStatement
    - Role
    - Standard
    - SupportiveEntity
    - Surrounding
    - TimeInstant
    range: string
  description:
    name: description
    description: The slot to provide a description for the Entity.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    slot_uri: dcterms:description
    alias: description
    owner: ChemicalEntity
    domain_of:
    - Activity
    - AgenticEntity
    - Any
    - Attribution
    - Catalogue
    - CatalogueRecord
    - ChecksumAlgorithm
    - Concept
    - ConceptScheme
    - DataService
    - Dataset
    - DatasetSeries
    - Distribution
    - Document
    - Entity
    - Frequency
    - Geometry
    - Identifier
    - LegalResource
    - LicenseDocument
    - LinguisticSystem
    - MediaType
    - MediaTypeOrExtent
    - PeriodOfTime
    - Plan
    - Policy
    - ProvenanceStatement
    - QualitativeAttribute
    - QuantitativeAttribute
    - Resource
    - RightsStatement
    - Role
    - Standard
    - SupportiveEntity
    - Surrounding
    - TimeInstant
    range: string
  id:
    name: id
    description: A slot to provide an URI for an entity within this schema.
    in_subset:
    - domain_agnostic_core
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    identifier: true
    alias: id
    owner: ChemicalEntity
    domain_of:
    - Activity
    - AgenticEntity
    - Dataset
    - DefinedTerm
    - Document
    - Entity
    - LegalResource
    - LicenseDocument
    - Resource
    range: uriorcurie
    required: true
  other_identifier:
    name: other_identifier
    description: A slot to provide a secondary identifier of the Entity.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    slot_uri: adms:identifier
    alias: other_identifier
    owner: ChemicalEntity
    domain_of:
    - Activity
    - AgenticEntity
    - Dataset
    - Entity
    range: Identifier
    required: false
    multivalued: true
    inlined_as_list: true
  has_qualitative_attribute:
    name: has_qualitative_attribute
    description: The slot to relate a qualitative attribute to an EvaluatedEntity,
      EvaluatedActivity or AgenticEntity
    in_subset:
    - domain_agnostic_core
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    slot_uri: dcterms:relation
    alias: has_qualitative_attribute
    owner: ChemicalEntity
    domain_of:
    - Activity
    - AgenticEntity
    - Entity
    range: QualitativeAttribute
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_quantitative_attribute:
    name: has_quantitative_attribute
    description: The slot to relate a quantitative attribute to an EvaluatedEntity,
      EvaluatedActivity or AgenticEntity
    in_subset:
    - domain_agnostic_core
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    slot_uri: dcterms:relation
    alias: has_quantitative_attribute
    owner: ChemicalEntity
    domain_of:
    - Activity
    - AgenticEntity
    - Entity
    range: QuantitativeAttribute
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_part:
    name: has_part
    description: The slot to provide the parts of a MaterialEntity.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    slot_uri: BFO:0000051
    alias: has_part
    owner: ChemicalEntity
    domain_of:
    - Activity
    - AgenticEntity
    - Catalogue
    - Entity
    range: MaterialEntity
    recommended: true
    multivalued: true
    inlined_as_list: true
  part_of:
    name: part_of
    description: The slot to specify an Entity of which the Entity is a part.
    notes:
    - not in DCAT-AP
    in_subset:
    - domain_agnostic_core
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    slot_uri: dcterms:isPartOf
    alias: part_of
    owner: ChemicalEntity
    domain_of:
    - Activity
    - AgenticEntity
    - Entity
    inverse: has_part
    range: Entity
    multivalued: true
    inlined_as_list: true
  type:
    name: type
    description: This slot is described in more detail within the class in which it
      is used.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    slot_uri: dcterms:type
    alias: type
    owner: ChemicalEntity
    domain_of:
    - Agent
    - ClassifierMixin
    - Dataset
    - LicenseDocument
    range: DefinedTerm
    inlined: true
  rdf_type:
    name: rdf_type
    description: The slot to specify the ontology class that is instantiated by an
      entity.
    in_subset:
    - domain_agnostic_core
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    slot_uri: rdf:type
    alias: rdf_type
    owner: ChemicalEntity
    domain_of:
    - ClassifierMixin
    range: DefinedTerm
    recommended: true
    inlined: true
class_uri: CHEBI:23367