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Class: ChemicalReaction

A process that leads to the transformation of one set of chemical substances to another.

URI: SIO:010345

classDiagram class ChemicalReaction click ChemicalReaction href "../ChemicalReaction/" Activity <|-- ChemicalReaction click Activity href "../Activity/" ChemicalReaction : carried_out_by ChemicalReaction --> "* _recommended_" AgenticEntity : carried_out_by click AgenticEntity href "../AgenticEntity/" ChemicalReaction : description ChemicalReaction : generated_product ChemicalReaction --> "* _recommended_" ChemicalProduct : generated_product click ChemicalProduct href "../ChemicalProduct/" ChemicalReaction : had_input_activity ChemicalReaction --> "* _recommended_" Activity : had_input_activity click Activity href "../Activity/" ChemicalReaction : had_input_entity ChemicalReaction --> "* _recommended_" Entity : had_input_entity click Entity href "../Entity/" ChemicalReaction : had_output_entity ChemicalReaction --> "* _recommended_" Entity : had_output_entity click Entity href "../Entity/" ChemicalReaction : has_duration ChemicalReaction : has_part ChemicalReaction --> "*" Activity : has_part click Activity href "../Activity/" ChemicalReaction : has_pressure ChemicalReaction --> "* _recommended_" Pressure : has_pressure click Pressure href "../Pressure/" ChemicalReaction : has_qualitative_attribute ChemicalReaction --> "* _recommended_" QualitativeAttribute : has_qualitative_attribute click QualitativeAttribute href "../QualitativeAttribute/" ChemicalReaction : has_quantitative_attribute ChemicalReaction --> "* _recommended_" QuantitativeAttribute : has_quantitative_attribute click QuantitativeAttribute href "../QuantitativeAttribute/" ChemicalReaction : has_reaction_step ChemicalReaction --> "0..1" ChemicalReaction : has_reaction_step click ChemicalReaction href "../ChemicalReaction/" ChemicalReaction : has_temperature ChemicalReaction --> "* _recommended_" Temperature : has_temperature click Temperature href "../Temperature/" ChemicalReaction : has_yield ChemicalReaction --> "* _recommended_" Yield : has_yield click Yield href "../Yield/" ChemicalReaction : id ChemicalReaction : other_identifier ChemicalReaction --> "*" Identifier : other_identifier click Identifier href "../Identifier/" ChemicalReaction : part_of ChemicalReaction --> "*" Activity : part_of click Activity href "../Activity/" ChemicalReaction : rdf_type ChemicalReaction --> "0..1 _recommended_" DefinedTerm : rdf_type click DefinedTerm href "../DefinedTerm/" ChemicalReaction : related_resource ChemicalReaction --> "*" Resource : related_resource click Resource href "../Resource/" ChemicalReaction : title ChemicalReaction : type ChemicalReaction --> "0..1" DefinedTerm : type click DefinedTerm href "../DefinedTerm/" ChemicalReaction : used_catalyst ChemicalReaction --> "* _recommended_" Catalyst : used_catalyst click Catalyst href "../Catalyst/" ChemicalReaction : used_reactant ChemicalReaction --> "* _recommended_" Reagent : used_reactant click Reagent href "../Reagent/" ChemicalReaction : used_reactor ChemicalReaction --> "* _recommended_" Reactor : used_reactor click Reactor href "../Reactor/" ChemicalReaction : used_solvent ChemicalReaction --> "* _recommended_" DissolvingSubstance : used_solvent click DissolvingSubstance href "../DissolvingSubstance/" ChemicalReaction : used_starting_material ChemicalReaction --> "* _recommended_" StartingMaterial : used_starting_material click StartingMaterial href "../StartingMaterial/"

Inheritance

Slots

Name Cardinality and Range Description Inheritance
used_starting_material * recommended
StartingMaterial		 The slot to specify the Reagent(s) of a ChemicalReaction direct
used_reactant * recommended
Reagent		 The slot to specify the Reagent(s) of a ChemicalReaction direct
generated_product * recommended
ChemicalProduct		 The slot to specify the Product of a ChemicalReaction direct
used_catalyst * recommended
Catalyst		 The slot to specify the Catalyst of a ChemicalReaction direct
used_solvent * recommended
DissolvingSubstance		 The slot to specify the chemical substance that had a solvent role (CHEBI:352... direct
has_duration 0..1
Duration		 A slot to provide the duration of a ChemicalReaction direct
used_reactor * recommended
Reactor		 The slot to specify the reactor used in a ChemicalReaction direct
has_temperature * recommended
Temperature		 The slot to specify the Temperature at which a ChemicalReaction takes place direct
has_pressure * recommended
Pressure		 The slot to specify the Pressure at which a ChemicalReaction takes place direct
has_yield * recommended
Yield		 A slot to provide the percentage of how much of the ChemicalProduct was produ... direct
has_reaction_step 0..1
ChemicalReaction		 A slot to specify a step (part) of a ChemicalReaction that is itself a Chemic... direct
related_resource *
Resource		 The slot to specify any Documents related to a ChemicalReaction direct
id 1
Uriorcurie		 A slot to provide an URI for an entity within this schema Activity
title *
String		 The slot to provide a title for the Activity Activity
description *
String		 The slot to provide a description for the Activity Activity
other_identifier *
Identifier		 The slot to provide a secondary identifier of the Activity Activity
has_part *
Activity		 The slot to provide an Activity that is part of the Activity Activity
had_input_entity * recommended
Entity		 The slot to specify the Entity that was used as an input of an Activity that ... Activity
had_output_entity * recommended
Entity		 The slot to specify the Entity that was generated as an output of an Activity Activity
had_input_activity * recommended
Activity		 The slot to provide a previous Activity that informed the Activity by being c... Activity
carried_out_by * recommended
AgenticEntity		 The slot to specify the AgenticEntity that played a certain part in carrying ... Activity
has_qualitative_attribute * recommended
QualitativeAttribute		 The slot to relate a qualitative attribute to an EvaluatedEntity, EvaluatedAc... Activity
has_quantitative_attribute * recommended
QuantitativeAttribute		 The slot to relate a quantitative attribute to an EvaluatedEntity, EvaluatedA... Activity
part_of *
Activity		 The slot to provide an Activity of which the Activity is a part Activity
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
ChemicalReaction has_reaction_step range ChemicalReaction

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 SIO:010345
native nmr_dcat_ap:ChemicalReaction
exact MOP:0000543, REX:0000002, AFP:0003711
narrow RXNO:0000329

LinkML Source

Direct

name: ChemicalReaction
description: A process that leads to the transformation of one set of chemical substances
  to another.
from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
exact_mappings:
- MOP:0000543
- REX:0000002
- AFP:0003711
narrow_mappings:
- RXNO:0000329
is_a: Activity
slots:
- used_starting_material
- used_reactant
- generated_product
- used_catalyst
- used_solvent
- has_duration
- used_reactor
- has_temperature
- has_pressure
- has_yield
- has_reaction_step
- related_resource
slot_usage:
  has_temperature:
    name: has_temperature
    description: The slot to specify the Temperature at which a ChemicalReaction takes
      place.
    inlined_as_list: true
  has_pressure:
    name: has_pressure
    description: The slot to specify the Pressure at which a ChemicalReaction takes
      place.
  related_resource:
    name: related_resource
    description: The slot to specify any Documents related to a ChemicalReaction.
    range: Resource
    multivalued: true
    inlined: true
    inlined_as_list: true
class_uri: SIO:010345

Induced

name: ChemicalReaction
description: A process that leads to the transformation of one set of chemical substances
  to another.
from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
exact_mappings:
- MOP:0000543
- REX:0000002
- AFP:0003711
narrow_mappings:
- RXNO:0000329
is_a: Activity
slot_usage:
  has_temperature:
    name: has_temperature
    description: The slot to specify the Temperature at which a ChemicalReaction takes
      place.
    inlined_as_list: true
  has_pressure:
    name: has_pressure
    description: The slot to specify the Pressure at which a ChemicalReaction takes
      place.
  related_resource:
    name: related_resource
    description: The slot to specify any Documents related to a ChemicalReaction.
    range: Resource
    multivalued: true
    inlined: true
    inlined_as_list: true
attributes:
  used_starting_material:
    name: used_starting_material
    description: The slot to specify the Reagent(s) of a ChemicalReaction.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    is_a: had_input_entity
    slot_uri: RO:0004009
    alias: used_starting_material
    owner: ChemicalReaction
    domain_of:
    - ChemicalReaction
    range: StartingMaterial
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  used_reactant:
    name: used_reactant
    description: The slot to specify the Reagent(s) of a ChemicalReaction.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    is_a: had_input_entity
    slot_uri: RO:0004009
    alias: used_reactant
    owner: ChemicalReaction
    domain_of:
    - ChemicalReaction
    range: Reagent
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  generated_product:
    name: generated_product
    description: The slot to specify the Product of a ChemicalReaction.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    is_a: had_output_entity
    slot_uri: RO:0004008
    alias: generated_product
    owner: ChemicalReaction
    domain_of:
    - ChemicalReaction
    range: ChemicalProduct
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  used_catalyst:
    name: used_catalyst
    description: The slot to specify the Catalyst of a ChemicalReaction.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    is_a: carried_out_by
    slot_uri: RXNO:0000425
    alias: used_catalyst
    owner: ChemicalReaction
    domain_of:
    - ChemicalReaction
    range: Catalyst
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  used_solvent:
    name: used_solvent
    description: The slot to specify the chemical substance that had a solvent role
      (CHEBI:35223) in a ChemicalReaction.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    is_a: carried_out_by
    slot_uri: prov:wasAssociatedWith
    alias: used_solvent
    owner: ChemicalReaction
    domain_of:
    - NMRSpectroscopy
    - ChemicalReaction
    range: DissolvingSubstance
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_duration:
    name: has_duration
    description: A slot to provide the duration of a ChemicalReaction.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    slot_uri: schema:duration
    alias: has_duration
    owner: ChemicalReaction
    domain_of:
    - ChemicalReaction
    range: duration
  used_reactor:
    name: used_reactor
    description: The slot to specify the reactor used in a ChemicalReaction.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    is_a: carried_out_by
    slot_uri: prov:wasAssociatedWith
    alias: used_reactor
    owner: ChemicalReaction
    domain_of:
    - ChemicalReaction
    range: Reactor
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_temperature:
    name: has_temperature
    description: The slot to specify the Temperature at which a ChemicalReaction takes
      place.
    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: ChemicalReaction
    domain_of:
    - Materialistic
    - ChemicalReaction
    range: Temperature
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_pressure:
    name: has_pressure
    description: The slot to specify the Pressure at which a ChemicalReaction takes
      place.
    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: ChemicalReaction
    domain_of:
    - Materialistic
    - ChemicalReaction
    range: Pressure
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_yield:
    name: has_yield
    description: A slot to provide the percentage of how much of the ChemicalProduct
      was produced by a ChemicalReaction.
    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_yield
    owner: ChemicalReaction
    domain_of:
    - ChemicalReaction
    range: Yield
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_reaction_step:
    name: has_reaction_step
    description: A slot to specify a step (part) of a ChemicalReaction that is itself
      a ChemicalReaction.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    is_a: has_part
    slot_uri: BFO:0000051
    alias: has_reaction_step
    owner: ChemicalReaction
    domain_of:
    - ChemicalReaction
    range: ChemicalReaction
  related_resource:
    name: related_resource
    description: The slot to specify any Documents related to a ChemicalReaction.
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    slot_uri: dcterms:relation
    alias: related_resource
    owner: ChemicalReaction
    domain_of:
    - Dataset
    - ChemicalReaction
    range: Resource
    multivalued: true
    inlined: true
    inlined_as_list: true
  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: ChemicalReaction
    domain_of:
    - Activity
    - AgenticEntity
    - Dataset
    - DefinedTerm
    - Document
    - Entity
    - LegalResource
    - LicenseDocument
    - Resource
    range: uriorcurie
    required: true
  title:
    name: title
    description: The slot to provide a title for the Activity.
    notes:
    - not in DCAT-AP
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    slot_uri: dcterms:title
    alias: title
    owner: ChemicalReaction
    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
    multivalued: true
    inlined_as_list: true
  description:
    name: description
    description: The slot to provide a description for the Activity.
    notes:
    - not in DCAT-AP
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    slot_uri: dcterms:description
    alias: description
    owner: ChemicalReaction
    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
    multivalued: true
    inlined_as_list: true
  other_identifier:
    name: other_identifier
    description: The slot to provide a secondary identifier of the Activity.
    notes:
    - not in DCAT-AP
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    slot_uri: adms:identifier
    alias: other_identifier
    owner: ChemicalReaction
    domain_of:
    - Activity
    - AgenticEntity
    - Dataset
    - Entity
    range: Identifier
    multivalued: true
    inlined_as_list: true
  has_part:
    name: has_part
    description: The slot to provide an Activity that is part of the Activity.
    notes:
    - not in DCAT-AP
    from_schema: https://NFDI4Chem.github.io/nmr-dcat-ap/nmr_dcat_ap.yaml
    rank: 1000
    slot_uri: dcterms:hasPart
    alias: has_part
    owner: ChemicalReaction
    domain_of:
    - Activity
    - AgenticEntity
    - Catalogue
    - Entity
    range: Activity
    multivalued: true
    inlined_as_list: true
  had_input_entity:
    name: had_input_entity
    description: The slot to specify the Entity that was used as an input of an Activity
      that is to be changed, consumed or transformed.
    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: prov:used
    alias: had_input_entity
    owner: ChemicalReaction
    domain_of:
    - Activity
    range: Entity
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  had_output_entity:
    name: had_output_entity
    description: The slot to specify the Entity that was generated as an output of
      an Activity.
    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: prov:generated
    alias: had_output_entity
    owner: ChemicalReaction
    domain_of:
    - Activity
    range: Entity
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  had_input_activity:
    name: had_input_activity
    description: The slot to provide a previous Activity that informed the Activity
      by being causally via a shared participant.
    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: prov:wasInformedBy
    alias: had_input_activity
    owner: ChemicalReaction
    domain_of:
    - Activity
    range: Activity
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  carried_out_by:
    name: carried_out_by
    description: The slot to specify the AgenticEntity that played a certain part
      in carrying out the Activity, either via having a specific role, function or
      disposition that was realized in the Activity.
    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: prov:wasAssociatedWith
    alias: carried_out_by
    owner: ChemicalReaction
    domain_of:
    - Activity
    range: AgenticEntity
    recommended: true
    multivalued: true
    inlined: 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
    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:relation
    alias: has_qualitative_attribute
    owner: ChemicalReaction
    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
    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:relation
    alias: has_quantitative_attribute
    owner: ChemicalReaction
    domain_of:
    - Activity
    - AgenticEntity
    - Entity
    range: QuantitativeAttribute
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  part_of:
    name: part_of
    description: The slot to provide an Activity of which the Activity 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: ChemicalReaction
    domain_of:
    - Activity
    - AgenticEntity
    - Entity
    inverse: has_part
    range: Activity
    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: ChemicalReaction
    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: ChemicalReaction
    domain_of:
    - ClassifierMixin
    range: DefinedTerm
    recommended: true
    inlined: true
class_uri: SIO:010345