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Class: isomerase reaction (IsomeraseReaction) (DEPRECATED)

A reaction that converts a molecule from one isomer to another.

URI: chemrof:IsomeraseReaction

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

      IsomeraseReaction : direction

      IsomeraseReaction : has_reaction_smiles_representation

      IsomeraseReaction : has_rinchi_representation

      IsomeraseReaction : id

      IsomeraseReaction : is_balanced

      IsomeraseReaction : is_diastereoselective

      IsomeraseReaction : is_fully_characterized

      IsomeraseReaction : is_stereo

      IsomeraseReaction : is_transport

      IsomeraseReaction : left_participants





        IsomeraseReaction --> "*" ReactionParticipant : left_participants
        click ReactionParticipant href "../ReactionParticipant/"



      IsomeraseReaction : name

      IsomeraseReaction : reaction_center

      IsomeraseReaction : reaction_rate

      IsomeraseReaction : reaction_rate_coefficient

      IsomeraseReaction : reaction_type





        IsomeraseReaction --> "0..1" ReactionTypeEnum : reaction_type
        click ReactionTypeEnum href "../ReactionTypeEnum/"



      IsomeraseReaction : right_participants





        IsomeraseReaction --> "*" ReactionParticipant : right_participants
        click ReactionParticipant href "../ReactionParticipant/"



      IsomeraseReaction : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
left_participants *
ReactionParticipant		 Reaction
right_participants *
ReactionParticipant		 Reaction
direction 0..1
String		 One of l->r, r->l, bidirectional, neutral Reaction
is_diastereoselective 0..1
Boolean		 Reaction
is_stereo 0..1
Boolean		 Reaction
is_balanced 0..1
Boolean		 Reaction
is_transport 0..1
Boolean		 Reaction
is_fully_characterized 0..1
Boolean		 False if includes R-groups Reaction
reaction_center 0..1
String		 Reaction
has_rinchi_representation 0..1
ChemicalEncoding		 Proposed Reactions InChI Reaction
has_reaction_smiles_representation 0..1
ChemicalEncoding		 Reaction
reaction_rate_coefficient 0..1
Float		 a proportionality constant that relates the reaction rate to reactant concent... Reaction
reaction_rate 0..1
Float		 the overall speed of a reaction, typically measured in concentration change p... Reaction
reaction_type 0..1
ReactionTypeEnum		 Classification of the chemical reaction based on mechanistic and functional c... Reaction
id 1
String		 DomainEntity
name 0..1
String		 name of chemical entity DomainEntity
type 0..1
Uriorcurie		 DomainEntity

Comments

  • This class is deprecated. Use the reaction_type slot with value 'isomerization' instead.

TODOs

  • create rules for this

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: IsomeraseReaction
description: A reaction that converts a molecule from one isomer to another.
title: isomerase reaction
deprecated: 'True'
todos:
- create rules for this
comments:
- This class is deprecated. Use the reaction_type slot with value 'isomerization'
  instead.
from_schema: https://w3id.org/chemrof
deprecated_element_has_exact_replacement: reaction_type
is_a: Reaction

Induced

name: IsomeraseReaction
description: A reaction that converts a molecule from one isomer to another.
title: isomerase reaction
deprecated: 'True'
todos:
- create rules for this
comments:
- This class is deprecated. Use the reaction_type slot with value 'isomerization'
  instead.
from_schema: https://w3id.org/chemrof
deprecated_element_has_exact_replacement: reaction_type
is_a: Reaction
attributes:
  left_participants:
    name: left_participants
    title: left participants
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: left_participants
    owner: IsomeraseReaction
    domain_of:
    - Reaction
    range: ReactionParticipant
    multivalued: true
  right_participants:
    name: right_participants
    title: right participants
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: right_participants
    owner: IsomeraseReaction
    domain_of:
    - Reaction
    range: ReactionParticipant
    multivalued: true
  direction:
    name: direction
    description: One of l->r, r->l, bidirectional, neutral
    title: direction
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: direction
    owner: IsomeraseReaction
    domain_of:
    - Reaction
    range: string
  is_diastereoselective:
    name: is_diastereoselective
    title: is diastereoselective
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: is_diastereoselective
    owner: IsomeraseReaction
    domain_of:
    - Reaction
    range: boolean
  is_stereo:
    name: is_stereo
    title: is stereo
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: is_stereo
    owner: IsomeraseReaction
    domain_of:
    - Reaction
    range: boolean
  is_balanced:
    name: is_balanced
    title: is balanced
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: is_balanced
    owner: IsomeraseReaction
    domain_of:
    - Reaction
    range: boolean
  is_transport:
    name: is_transport
    title: is transport
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: is_transport
    owner: IsomeraseReaction
    domain_of:
    - Reaction
    range: boolean
  is_fully_characterized:
    name: is_fully_characterized
    description: False if includes R-groups
    title: is fully characterized
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: is_fully_characterized
    owner: IsomeraseReaction
    domain_of:
    - Reaction
    range: boolean
  reaction_center:
    name: reaction_center
    title: reaction center
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: reaction_center
    owner: IsomeraseReaction
    domain_of:
    - Reaction
    range: string
  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_representation
    domain: ChemicalEntity
    alias: has_rinchi_representation
    owner: IsomeraseReaction
    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: has_reaction_representation
    domain: ChemicalEntity
    alias: has_reaction_smiles_representation
    owner: IsomeraseReaction
    domain_of:
    - Reaction
    range: ChemicalEncoding
  reaction_rate_coefficient:
    name: reaction_rate_coefficient
    description: a proportionality constant that relates the reaction rate to reactant
      concentrations.
    title: reaction rate coefficient
    from_schema: https://w3id.org/chemrof
    aliases:
    - reaction rate constant
    rank: 1000
    alias: reaction_rate_coefficient
    owner: IsomeraseReaction
    domain_of:
    - Reaction
    range: float
  reaction_rate:
    name: reaction_rate
    description: the overall speed of a reaction, typically measured in concentration
      change per unit time
    title: reaction rate
    from_schema: https://w3id.org/chemrof
    aliases:
    - v
    rank: 1000
    alias: reaction_rate
    owner: IsomeraseReaction
    domain_of:
    - Reaction
    range: float
    unit:
      symbol: mol⋅m-3⋅s-1
  reaction_type:
    name: reaction_type
    description: Classification of the chemical reaction based on mechanistic and
      functional categories
    title: reaction type
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: reaction_type
    owner: IsomeraseReaction
    domain_of:
    - Reaction
    range: ReactionTypeEnum
  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: IsomeraseReaction
    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: IsomeraseReaction
    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: IsomeraseReaction
    domain_of:
    - DomainEntity
    range: uriorcurie