Skip to content

Class: reaction (Reaction)

Reaction

URI: chemrof:Reaction

 classDiagram
    class Reaction
    click Reaction href "../Reaction"
      DomainEntity <|-- Reaction
        click DomainEntity href "../DomainEntity"


      Reaction <|-- IsomeraseReaction
        click IsomeraseReaction href "../IsomeraseReaction"


      Reaction : has_reaction_smiles_representation

      Reaction : has_rinchi_representation

      Reaction : id

      Reaction : name

      Reaction : reaction_rate

      Reaction : reaction_rate_coefficient

      Reaction : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
has_rinchi_representation 0..1
ChemicalEncoding		 Proposed Reactions InChI direct
has_reaction_smiles_representation 0..1
ChemicalEncoding		 direct
reaction_rate_coefficient 0..1
Float		 direct
reaction_rate 0..1
Float		 direct
id 1
String		 DomainEntity
name 0..1
String		 name of chemical entity DomainEntity
type 0..1
Uriorcurie		 DomainEntity

TODOs

  • Align with https://docs.open-reaction-database.org/en/latest/schema.html

Identifier and Mapping Information

Valid ID Prefixes

Instances of this class should have identifiers with one of the following prefixes:

  • RHEA

  • KEGG.REACTION

  • GO

  • MetaCyc

  • REACT

  • EC

  • MetaNetX.reaction

  • SEED

  • RetroRules

  • RXNO

  • MOP

  • REX

Schema Source

  • from schema: https://w3id.org/chemrof

Mappings

Mapping Type Mapped Value
self chemrof:Reaction
native chemrof:Reaction

LinkML Source

Direct

name: Reaction
id_prefixes:
- RHEA
- KEGG.REACTION
- GO
- MetaCyc
- REACT
- EC
- MetaNetX.reaction
- SEED
- RetroRules
- RXNO
- MOP
- REX
description: Reaction
title: reaction
todos:
- Align with https://docs.open-reaction-database.org/en/latest/schema.html
from_schema: https://w3id.org/chemrof
is_a: DomainEntity
slots:
- has_rinchi_representation
- has_reaction_smiles_representation
- reaction_rate_coefficient
- reaction_rate
slot_usage:
  left_participants:
    name: left_participants
    range: ReactionParticipant
    multivalued: true
  right_participants:
    name: right_participants
    range: ReactionParticipant
    multivalued: true
  direction:
    name: direction
    description: One of l->r, r->l, bidirectional, neutral
  smarts_string:
    name: smarts_string
    range: string
  is_diastereoselective:
    name: is_diastereoselective
    range: boolean
  is_stereo:
    name: is_stereo
    range: boolean
  is_balanced:
    name: is_balanced
    range: boolean
  is_transport:
    name: is_transport
    range: boolean
  is_fully_characterized:
    name: is_fully_characterized
    description: False if includes R-groups
    range: boolean
  reaction_center:
    name: reaction_center
  description:
    name: description
    string_serialization: '{left participants} {direction} {right participants}'

Induced

name: Reaction
id_prefixes:
- RHEA
- KEGG.REACTION
- GO
- MetaCyc
- REACT
- EC
- MetaNetX.reaction
- SEED
- RetroRules
- RXNO
- MOP
- REX
description: Reaction
title: reaction
todos:
- Align with https://docs.open-reaction-database.org/en/latest/schema.html
from_schema: https://w3id.org/chemrof
is_a: DomainEntity
slot_usage:
  left_participants:
    name: left_participants
    range: ReactionParticipant
    multivalued: true
  right_participants:
    name: right_participants
    range: ReactionParticipant
    multivalued: true
  direction:
    name: direction
    description: One of l->r, r->l, bidirectional, neutral
  smarts_string:
    name: smarts_string
    range: string
  is_diastereoselective:
    name: is_diastereoselective
    range: boolean
  is_stereo:
    name: is_stereo
    range: boolean
  is_balanced:
    name: is_balanced
    range: boolean
  is_transport:
    name: is_transport
    range: boolean
  is_fully_characterized:
    name: is_fully_characterized
    description: False if includes R-groups
    range: boolean
  reaction_center:
    name: reaction_center
  description:
    name: description
    string_serialization: '{left participants} {direction} {right participants}'
attributes:
  has_rinchi_representation:
    name: has_rinchi_representation
    description: Proposed Reactions InChI
    title: has rinchi representation
    comments:
    - A half-reaction, such as a RInChI with starting materials and no identified
      products, is a valid RInChI
    examples:
    - value: RInChI=1.00.1S /layer2<>layer3<>layer4/d+/u2-0-1
    - value: 'C2H4O2/c1-2(3)4/h1H3,(H,3,4)!C2H6O/c1-2-3/h3H,2H2,1H3<>C4H8O2/c1-3-6-4(2)5/h3H2,1-
        2H3!H2O/h1H2<>H2O4S/c1-5(2,3)4/h(H2,1,2,3,4):'
      description: hydrolysis of ethyl acetate
    from_schema: https://w3id.org/chemrof
    see_also:
    - https://jcheminf.biomedcentral.com/articles/10.1186/s13321-018-0277-8
    aliases:
    - RInChi
    rank: 1000
    is_a: chemical_formula
    domain: ChemicalEntity
    alias: has_rinchi_representation
    owner: Reaction
    domain_of:
    - Reaction
    range: ChemicalEncoding
  has_reaction_smiles_representation:
    name: has_reaction_smiles_representation
    title: has reaction smiles representation
    from_schema: https://w3id.org/chemrof
    aliases:
    - reaction SMILES
    rank: 1000
    is_a: chemical_formula
    domain: ChemicalEntity
    alias: has_reaction_smiles_representation
    owner: Reaction
    domain_of:
    - Reaction
    range: ChemicalEncoding
  reaction_rate_coefficient:
    name: reaction_rate_coefficient
    title: reaction rate coefficient
    from_schema: https://w3id.org/chemrof
    aliases:
    - reaction rate constant
    rank: 1000
    alias: reaction_rate_coefficient
    owner: Reaction
    domain_of:
    - Reaction
    range: float
  reaction_rate:
    name: reaction_rate
    title: reaction rate
    from_schema: https://w3id.org/chemrof
    aliases:
    - v
    rank: 1000
    alias: reaction_rate
    owner: Reaction
    domain_of:
    - Reaction
    range: float
    unit:
      symbol: mol⋅m-3⋅s-1
  id:
    name: id
    title: id
    from_schema: https://w3id.org/chemrof
    mappings:
    - schema:identifier
    rank: 1000
    is_a: information_property
    identifier: true
    alias: id
    owner: Reaction
    domain_of:
    - DomainEntity
    - GroupingClass
    - ChemicalGroupingClass
    range: string
    required: true
  name:
    name: name
    description: name of chemical entity. E.g. nickel, carbon-16
    title: name
    from_schema: https://w3id.org/chemrof
    close_mappings:
    - bo:symbol
    rank: 1000
    is_a: information_property
    slot_uri: rdfs:label
    alias: name
    owner: Reaction
    domain_of:
    - DomainEntity
    - GroupingClass
    - Atom
    - AtomOccurrence
    range: string
  type:
    name: type
    title: type
    from_schema: https://w3id.org/chemrof
    rank: 1000
    designates_type: true
    alias: type
    owner: Reaction
    domain_of:
    - DomainEntity
    range: uriorcurie