Class: Atom

A MaterialEntity constituting the smallest component of an element having the chemical properties of the element.

 classDiagram
    class Atom
    click Atom href "../../classes/Atom/"
      ChemicalEntity <|-- Atom
        click ChemicalEntity href "../../classes/ChemicalEntity/"

      Atom : alternative_label

      Atom : description

      Atom : has_density





        Atom --> "* _recommended_" Density : has_density
        click Density href "../../classes/Density/"



      Atom : has_mass





        Atom --> "* _recommended_" Mass : has_mass
        click Mass href "../../classes/Mass/"



      Atom : has_molar_mass





        Atom --> "* _recommended_" MolarMass : has_molar_mass
        click MolarMass href "../../classes/MolarMass/"



      Atom : has_part





        Atom --> "* _recommended_" MaterialEntity : has_part
        click MaterialEntity href "../../classes/MaterialEntity/"



      Atom : has_physical_state





        Atom --> "0..1" PhysicalStateEnum : has_physical_state
        click PhysicalStateEnum href "../../enums/PhysicalStateEnum/"



      Atom : has_pressure





        Atom --> "* _recommended_" Pressure : has_pressure
        click Pressure href "../../classes/Pressure/"



      Atom : has_qualitative_attribute





        Atom --> "* _recommended_" QualitativeAttribute : has_qualitative_attribute
        click QualitativeAttribute href "../../classes/QualitativeAttribute/"



      Atom : has_quantitative_attribute





        Atom --> "* _recommended_" QuantitativeAttribute : has_quantitative_attribute
        click QuantitativeAttribute href "../../classes/QuantitativeAttribute/"



      Atom : has_temperature





        Atom --> "* _recommended_" Temperature : has_temperature
        click Temperature href "../../classes/Temperature/"



      Atom : has_volume





        Atom --> "* _recommended_" Volume : has_volume
        click Volume href "../../classes/Volume/"



      Atom : id

      Atom : inchi





        Atom --> "* _recommended_" InChi : inchi
        click InChi href "../../classes/InChi/"



      Atom : inchikey





        Atom --> "* _recommended_" InChIKey : inchikey
        click InChIKey href "../../classes/InChIKey/"



      Atom : iupac_name





        Atom --> "* _recommended_" IUPACName : iupac_name
        click IUPACName href "../../classes/IUPACName/"



      Atom : molecular_formula





        Atom --> "* _recommended_" MolecularFormula : molecular_formula
        click MolecularFormula href "../../classes/MolecularFormula/"



      Atom : other_identifier





        Atom --> "*" Identifier : other_identifier
        click Identifier href "../../classes/Identifier/"



      Atom : part_of





        Atom --> "*" Entity : part_of
        click Entity href "../../classes/Entity/"



      Atom : rdf_type





        Atom --> "1 _recommended_" DefinedTerm : rdf_type
        click DefinedTerm href "../../classes/DefinedTerm/"



      Atom : smiles





        Atom --> "* _recommended_" SMILES : smiles
        click SMILES href "../../classes/SMILES/"



      Atom : title

      Atom : type





        Atom --> "0..1" DefinedTerm : type
        click DefinedTerm href "../../classes/DefinedTerm/"

Inheritance

Entity [ ClassifierMixin]
- MaterialEntity [ Materialistic]
  - ChemicalEntity
    - Atom

Slots

Name	Cardinality and Range	Description	Inheritance
inchi	* recommended InChi	The slot to provide the InChi descriptor of a ChemicalEntity.	ChemicalEntity
inchikey	* recommended InChIKey	The slot to provide the InChiKey of a ChemicalEntity.	ChemicalEntity
smiles	* recommended SMILES	The slot to provide the canonical SMILES descriptor of a ChemicalEntity.	ChemicalEntity
molecular_formula	* recommended MolecularFormula	The slot to provide the IUPAC formula of a ChemicalEntity.	ChemicalEntity
iupac_name	* recommended IUPACName	The slot to provide the IUPAC name of a ChemicalEntity.	ChemicalEntity
has_molar_mass	* recommended MolarMass	The slot to provide the MolarMass of a ChemicalEntity.	ChemicalEntity
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, EvaluatedActivity or AgenticEntity	Entity
has_quantitative_attribute	* recommended QuantitativeAttribute	The slot to relate a quantitative attribute to an EvaluatedEntity, EvaluatedActivity or AgenticEntity	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	1 recommended DefinedTerm	The slot to provide the Atom as a ChEBI ID from the atom (CHEBI:33250) branch.	ClassifierMixin

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/nfdi-de/dcat-ap-plus/chemistry

Mappings

Mapping Type	Mapped Value
self	CHEBI:33250
native	chemdcatap:Atom

LinkML Source

Direct

name: Atom
description: A MaterialEntity constituting the smallest component of an element having
  the chemical properties of the element.
from_schema: https://w3id.org/nfdi-de/dcat-ap-plus/chemistry
is_a: ChemicalEntity
slot_usage:
  rdf_type:
    name: rdf_type
    description: The slot to provide the Atom as a ChEBI ID from the atom (CHEBI:33250)
      branch.
    required: true
class_uri: CHEBI:33250

Induced

name: Atom
description: A MaterialEntity constituting the smallest component of an element having
  the chemical properties of the element.
from_schema: https://w3id.org/nfdi-de/dcat-ap-plus/chemistry
is_a: ChemicalEntity
slot_usage:
  rdf_type:
    name: rdf_type
    description: The slot to provide the Atom as a ChEBI ID from the atom (CHEBI:33250)
      branch.
    required: true
attributes:
  inchi:
    name: inchi
    description: The slot to provide the InChi descriptor of a ChemicalEntity.
    from_schema: https://w3id.org/nfdi-de/dcat-ap-plus/chemistry
    rank: 1000
    is_a: has_qualitative_attribute
    slot_uri: SIO:000008
    alias: inchi
    owner: Atom
    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://w3id.org/nfdi-de/dcat-ap-plus/chemistry
    rank: 1000
    is_a: has_qualitative_attribute
    slot_uri: SIO:000008
    alias: inchikey
    owner: Atom
    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://w3id.org/nfdi-de/dcat-ap-plus/chemistry
    rank: 1000
    is_a: has_qualitative_attribute
    slot_uri: SIO:000008
    alias: smiles
    owner: Atom
    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://w3id.org/nfdi-de/dcat-ap-plus/chemistry
    rank: 1000
    is_a: has_qualitative_attribute
    slot_uri: SIO:000008
    alias: molecular_formula
    owner: Atom
    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://w3id.org/nfdi-de/dcat-ap-plus/chemistry
    rank: 1000
    is_a: has_qualitative_attribute
    slot_uri: SIO:000008
    alias: iupac_name
    owner: Atom
    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://w3id.org/nfdi-de/dcat-ap-plus/chemistry
    rank: 1000
    is_a: has_mass
    slot_uri: SIO:000008
    alias: has_molar_mass
    owner: Atom
    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://w3id.org/nfdi-de/dcat-ap-plus/chemistry
    rank: 1000
    slot_uri: skos:altLabel
    alias: alternative_label
    owner: Atom
    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://w3id.org/nfdi-de/dcat-ap-plus/chemistry
    rank: 1000
    slot_uri: SIO:000008
    alias: has_physical_state
    owner: Atom
    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://w3id.org/nfdi-de/dcat-ap-plus/chemistry
    rank: 1000
    is_a: has_quantitative_attribute
    slot_uri: SIO:000008
    alias: has_temperature
    owner: Atom
    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://w3id.org/nfdi-de/dcat-ap-plus/chemistry
    rank: 1000
    is_a: has_quantitative_attribute
    slot_uri: SIO:000008
    alias: has_mass
    owner: Atom
    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://w3id.org/nfdi-de/dcat-ap-plus/chemistry
    rank: 1000
    is_a: has_quantitative_attribute
    slot_uri: SIO:000008
    alias: has_volume
    owner: Atom
    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://w3id.org/nfdi-de/dcat-ap-plus/chemistry
    rank: 1000
    is_a: has_quantitative_attribute
    slot_uri: SIO:000008
    alias: has_density
    owner: Atom
    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://w3id.org/nfdi-de/dcat-ap-plus/chemistry
    rank: 1000
    is_a: has_quantitative_attribute
    slot_uri: SIO:000008
    alias: has_pressure
    owner: Atom
    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://w3id.org/nfdi-de/dcat-ap-plus/chemistry
    rank: 1000
    slot_uri: dcterms:title
    alias: title
    owner: Atom
    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://w3id.org/nfdi-de/dcat-ap-plus/chemistry
    rank: 1000
    slot_uri: dcterms:description
    alias: description
    owner: Atom
    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://w3id.org/nfdi-de/dcat-ap-plus/chemistry
    rank: 1000
    identifier: true
    alias: id
    owner: Atom
    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://w3id.org/nfdi-de/dcat-ap-plus/chemistry
    rank: 1000
    slot_uri: adms:identifier
    alias: other_identifier
    owner: Atom
    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://w3id.org/nfdi-de/dcat-ap-plus/chemistry
    rank: 1000
    slot_uri: dcterms:relation
    alias: has_qualitative_attribute
    owner: Atom
    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://w3id.org/nfdi-de/dcat-ap-plus/chemistry
    rank: 1000
    slot_uri: dcterms:relation
    alias: has_quantitative_attribute
    owner: Atom
    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://w3id.org/nfdi-de/dcat-ap-plus/chemistry
    rank: 1000
    slot_uri: BFO:0000051
    alias: has_part
    owner: Atom
    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://w3id.org/nfdi-de/dcat-ap-plus/chemistry
    rank: 1000
    slot_uri: dcterms:isPartOf
    alias: part_of
    owner: Atom
    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://w3id.org/nfdi-de/dcat-ap-plus/chemistry
    rank: 1000
    slot_uri: dcterms:type
    alias: type
    owner: Atom
    domain_of:
    - Agent
    - ClassifierMixin
    - Dataset
    - LicenseDocument
    range: DefinedTerm
    inlined: true
  rdf_type:
    name: rdf_type
    description: The slot to provide the Atom as a ChEBI ID from the atom (CHEBI:33250)
      branch.
    in_subset:
    - domain_agnostic_core
    from_schema: https://w3id.org/nfdi-de/dcat-ap-plus/chemistry
    rank: 1000
    slot_uri: rdf:type
    alias: rdf_type
    owner: Atom
    domain_of:
    - ClassifierMixin
    range: DefinedTerm
    required: true
    recommended: true
    inlined: true
class_uri: CHEBI:33250