---
id: https://HendrikBorgelt.github.io/test_chemDCAT_ap_versioning_freeze/chemistry/reaction/v0.4.5/
name: chemical-reaction-ap
title: Chemical Reaction Application Profile
description: |-
  This is an application profile for chemical reactions that is intended to be used as an extension of DCAT-AP-PLUS.
license: CC-BY 4.0
prefixes:
  chemical_reaction_ap: https://HendrikBorgelt.github.io/test_chemDCAT_ap_versioning_freeze/chemistry/reaction/v0.4.5/
  chemdcatap: https://HendrikBorgelt.github.io/test_chemDCAT_ap_versioning_freeze/v0.4.5/
  dcatapplus: https://HendrikBorgelt.github.io/test_dcat_ap_plus_versioning_freeze/v0.5.0/
  linkml: https://w3id.org/linkml/
  biolink: https://w3id.org/biolink/vocab/
  schema: http://schema.org/
  dcterms: http://purl.org/dc/terms/
  dcat: http://www.w3.org/ns/dcat#
  prov: http://www.w3.org/ns/prov#
  sosa: http://www.w3.org/ns/sosa/
  vcard: http://www.w3.org/2006/vcard/ns#
  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
  rdfs: http://www.w3.org/2000/01/rdf-schema#
  owl: http://www.w3.org/2002/07/owl#
  skos: http://www.w3.org/2004/02/skos/core#
  foaf: http://xmlns.com/foaf/0.1/
  qudt: http://qudt.org/schema/qudt/
  RO: http://purl.obolibrary.org/obo/RO_
  PATO: http://purl.obolibrary.org/obo/PATO_
  OBI: http://purl.obolibrary.org/obo/OBI_
  IAO: http://purl.obolibrary.org/obo/IAO_
  CHEBI: http://purl.obolibrary.org/obo/CHEBI_
  CHMO: http://purl.obolibrary.org/obo/CHMO_
  BFO: http://purl.obolibrary.org/obo/BFO_
  T4FS: http://purl.obolibrary.org/obo/T4FS_
  FOODON: http://purl.obolibrary.org/obo/FOODON_
  CHEMINF: http://semanticscience.org/resource/CHEMINF_
  RXNO: http://purl.obolibrary.org/obo/RXNO_
  MOP: http://purl.obolibrary.org/obo/MOP_
  ex: http://example.org/
  NCIT: http://purl.obolibrary.org/obo/NCIT_
  SIO: http://semanticscience.org/resource/SIO_
  doi: https://doi.org/
  NMR: "http://nmrML.org/nmrCV#NMR:"
  AFE: http://purl.allotrope.org/ontologies/equipment#AFE_
  AFRL: http://purl.allotrope.org/ontologies/role#AFRL_
  AFP: http://purl.allotrope.org/ontologies/process#AFP_
  VOC4CAT: https://w3id.org/nfdi4cat/voc4cat_
  PROCO: http://purl.obolibrary.org/obo/PROCO_
  time: http://www.w3.org/2006/time#
  REX: http://purl.obolibrary.org/obo/REX_
  ENVO: http://purl.obolibrary.org/obo/ENVO_
default_prefix: chemical_reaction_ap
default_range: string
imports:
  - linkml:types
  - dcatapplus:schema/dcat_ap_plus
  - chemdcatap:schema/chemical_entities_ap

classes:

  ChemicalReaction:
    is_a: EvaluatedActivity
    class_uri: SIO:010345
    description: A process that leads to the transformation of one set of chemical substances to another and that is the subject matter of a DataGeneratingActivity.
    slots:
      - used_starting_material
      - used_reactant
      - generated_product
      - used_catalyst
      - used_solvent
      - has_duration
      - used_reactor
      - has_temperature # reused from material_entities_ap.yaml
      - has_pressure # reused from material_entities_ap.yaml
      - has_yield
      - has_reaction_step
      - related_resource
    slot_usage:
      has_temperature:
        description: The slot to specify the Temperature at which a ChemicalReaction takes place.
        inlined_as_list: true
      has_pressure:
        description: The slot to specify the Pressure at which a ChemicalReaction takes place.
      related_resource:
        range: Resource
        multivalued: true
        inlined: true
        inlined_as_list: true
        description: The slot to specify any Documents related to a ChemicalReaction.
    exact_mappings:
      - MOP:0000543
      - REX:0000002
      - AFP:0003711
    narrow_mappings:
      - RXNO:0000329

  StartingMaterial:
    class_uri: PROCO:0000029
    is_a: MaterialEntity
    mixins:
      - ChemicalSubstanceMixin
    description: A ChemicalSubstance with that has a starting material role in a synthesis.
    slots:
      - has_molar_equivalent

  DissolvingSubstance:
    class_uri: SIO:010417
    is_a: AgenticEntity
    aliases:
      - solvent
    slots:
      - has_percentage_of_total
    mixins:
      - ChemicalSubstanceMixin
    description: A liquid ChemicalSubstance that dissolves or that is capable of dissolving a ChemicalSubstance.
    exact_mappings:
      - VOC4CAT:0007246
      - NCIT:C45790

  Reagent:
    class_uri: SIO:010411
    is_a: MaterialEntity
    mixins:
      - ChemicalSubstanceMixin
    description: A ChemicalSubstance that is consumed or transformed in a ChemicalReaction.
    slots:
      - has_molar_equivalent
    exact_mappings:
      - NCIT:C802
      - VOC4CAT:0000101
    close_mappings:
      - OBI:0001879
      - PROCO:0000029

  ChemicalProduct:
    class_uri: NCIT:C48810
    is_a: MaterialEntity
    mixins:
      - ChemicalSubstanceMixin
    description: A chemical substance that is produced by a ChemicalReaction.
    exact_mappings:
      - VOC4CAT:0000194
    close_mappings:
      - ENVO:2000000

  Catalyst:
    class_uri: SIO:010344
    is_a: AgenticEntity
    mixins:
      - ChemicalSubstanceMixin
    description: A ChemicalSubstance or MaterialEntity that initiates or accelerates a ChemicalReaction without itself being affected.
    slots:
      - has_molar_equivalent
    exact_mappings:
      - VOC4CAT:0000194
      - NCIT:C48810
    close_mappings:
      - CHEBI:35223

  Reactor:
    is_a: Device
    class_uri: AFE:0000153
    mixins:
      - MaterialisticMixin
    description: A reactor is a container for controlling a biological or chemical reaction or process.
    exact_mappings:
      - VOC4CAT:0007017

  Yield:
    class_uri: CHMO:0002855
    is_a: QuantitativeAttribute
    description: A dimensionless physical quantity describing the fraction of a product B that is formed from a reactant A taking into account the stoichiometry. If A fully reacts to B without side-reactions, the yield of product B is 1 (or 100 %).
    exact_mappings:
      - VOC4CAT:0005005

  MolarEquivalent:
    class_uri: qudt:Quantity
    is_a: QuantitativeAttribute
    description: A dimensionless ratio that quantifies the stoichiometric proportion of a chemical substance relative to a reference substance in a chemical reaction.

  PercentageOfTotal:
    class_uri: qudt:Quantity
    is_a: QuantitativeAttribute
    description: A dimensionless ratio that quantifies the stoichiometric proportion of a chemical substance relative to a reference substance in a chemical reaction.
      #slot_usage:
      #has_quantity_type:
      # ifabsent: http://qudt.org/vocab/quantitykind/Dimensionless
    #unit:
    # ifabsent: https://qudt.org/vocab/unit/MilliL

slots:
  used_starting_material:
    range: StartingMaterial
    is_a: had_input_entity
    slot_uri: RO:0004009
    description: The slot to specify the StartingMaterial(s) of a ChemicalReaction.
    multivalued: true
    inlined_as_list: true
    recommended: true
  used_reactant:
    range: Reagent
    is_a: had_input_entity
    slot_uri: RO:0004009
    description: The slot to specify the Reagent(s) of a ChemicalReaction.
    multivalued: true
    inlined_as_list: true
    recommended: true
  generated_product:
    range: ChemicalProduct
    is_a: had_output_entity
    slot_uri: RO:0004008
    description: The slot to specify the Product(s) of a ChemicalReaction.
    multivalued: true
    inlined_as_list: true
    recommended: true
  used_catalyst:
    range: Catalyst
    is_a: carried_out_by
    slot_uri: RXNO:0000425
    description: The slot to specify the Catalyst of a ChemicalReaction.
    multivalued: true
    inlined_as_list: true
    recommended: true
  used_solvent:
    range: DissolvingSubstance
    is_a: carried_out_by
    slot_uri: prov:wasAssociatedWith
    description: The slot to specify the chemical substance that had a solvent role (CHEBI:35223) in a ChemicalReaction.
    recommended: true
    multivalued: true
    inlined_as_list: true
  has_duration:
    slot_uri: schema:duration
    range: duration
    description: A slot to provide the duration of a ChemicalReaction.
  used_reactor:
    is_a: carried_out_by
    slot_uri: prov:wasAssociatedWith
    description: The slot to specify the reactor used in a ChemicalReaction.
    range: Reactor
  has_yield:
    slot_uri: SIO:000008
    is_a: has_quantitative_attribute
    description: A slot to provide the percentage of how much of the ChemicalProduct was produced by a ChemicalReaction.
    range: Yield
  has_molar_equivalent:
    slot_uri: SIO:000008 # using SIO here instead of dcterms:relation of DCAT-AP-PLUS
    is_a: has_quantitative_attribute
    range: MolarEquivalent
    description: A slot to provide the MolarEquivalent of a ChemicalSubstance, such as the DissolvingSubstance, Starting Material or Reactant, within the context of a chemical reaction.
  has_percentage_of_total:
    slot_uri: SIO:000008 # using SIO here instead of dcterms:relation of DCAT-AP-PLUS
    is_a: has_quantitative_attribute
    range: PercentageOfTotal
    description:
      A slot to specify the percentage of a specific ChemicalSubstance in relation to the total amount of that same substance used across a multi-step reaction.
  has_reaction_step:
    is_a: has_part
    slot_uri: BFO:0000051
    description: A slot to specify a step (part) of a ChemicalReaction that is itself a ChemicalReaction.
    range: ChemicalReaction
    multivalued: true
    inlined_as_list: true