Class: Reaction

An individual biochemical transformation carried out by a functional unit of an organism, in which a collection of substrates are transformed into a collection of products. Can also represent transporters

URI: nmdc:Reaction

classDiagram class Reaction click Reaction href "../Reaction" FunctionalAnnotationTerm <|-- Reaction click FunctionalAnnotationTerm href "../FunctionalAnnotationTerm" Reaction : alternative_identifiers Reaction : description Reaction : direction Reaction : id Reaction : is_balanced Reaction : is_diastereoselective Reaction : is_fully_characterized Reaction : is_stereo Reaction : is_transport Reaction : left_participants Reaction --> "*" ReactionParticipant : left_participants click ReactionParticipant href "../ReactionParticipant" Reaction : name Reaction : right_participants Reaction --> "*" ReactionParticipant : right_participants click ReactionParticipant href "../ReactionParticipant" Reaction : smarts_string

Inheritance

NamedThing
- OntologyClass
  - FunctionalAnnotationTerm
    - Reaction

Slots

Name	Cardinality and Range	Description	Inheritance
direction	0..1 String	One of l->r, r->l, bidirectional, neutral	direct
is_balanced	0..1 Boolean		direct
is_diastereoselective	0..1 Boolean		direct
is_fully_characterized	0..1 Boolean	False if includes R-groups	direct
is_stereo	0..1 Boolean		direct
is_transport	0..1 Boolean		direct
left_participants	0..* ReactionParticipant		direct
right_participants	0..* ReactionParticipant		direct
smarts_string	0..1 String		direct
id	1..1 Uriorcurie	A unique identifier for a thing	NamedThing
name	0..1 String	A human readable label for an entity	NamedThing
description	0..1 String	a human-readable description of a thing	NamedThing
alternative_identifiers	0..* Uriorcurie	A list of alternative identifiers for the entity	NamedThing

Usages

used by	used in	type	used
Pathway	has_part	range	Reaction
Reaction	direction	domain	Reaction
Reaction	left_participants	domain	Reaction
Reaction	right_participants	domain	Reaction

Identifier and Mapping Information

Valid ID Prefixes

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

KEGG.REACTION
RHEA
MetaCyc
EC
GO
MetaNetX
SEED
RetroRules

Schema Source

from schema: https://w3id.org/nmdc/nmdc

Mappings

Mapping Type	Mapped Value
self	nmdc:Reaction
native	nmdc:Reaction
exact	biolink:MolecularActivity

LinkML Source

Direct

name: Reaction
id_prefixes:
- KEGG.REACTION
- RHEA
- MetaCyc
- EC
- GO
- MetaNetX
- SEED
- RetroRules
description: An individual biochemical transformation carried out by a functional
  unit of an organism, in which a collection of substrates are transformed into a
  collection of products. Can also represent transporters
from_schema: https://w3id.org/nmdc/nmdc
exact_mappings:
- biolink:MolecularActivity
is_a: FunctionalAnnotationTerm
slots:
- direction
- is_balanced
- is_diastereoselective
- is_fully_characterized
- is_stereo
- is_transport
- left_participants
- right_participants
- smarts_string

Induced

name: Reaction
id_prefixes:
- KEGG.REACTION
- RHEA
- MetaCyc
- EC
- GO
- MetaNetX
- SEED
- RetroRules
description: An individual biochemical transformation carried out by a functional
  unit of an organism, in which a collection of substrates are transformed into a
  collection of products. Can also represent transporters
from_schema: https://w3id.org/nmdc/nmdc
exact_mappings:
- biolink:MolecularActivity
is_a: FunctionalAnnotationTerm
attributes:
  direction:
    name: direction
    description: One of l->r, r->l, bidirectional, neutral
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    domain: Reaction
    alias: direction
    owner: Reaction
    domain_of:
    - Reaction
    range: string
  is_balanced:
    name: is_balanced
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: is_balanced
    owner: Reaction
    domain_of:
    - Reaction
    range: boolean
  is_diastereoselective:
    name: is_diastereoselective
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: is_diastereoselective
    owner: Reaction
    domain_of:
    - Reaction
    range: boolean
  is_fully_characterized:
    name: is_fully_characterized
    description: False if includes R-groups
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: is_fully_characterized
    owner: Reaction
    domain_of:
    - Reaction
    range: boolean
  is_stereo:
    name: is_stereo
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: is_stereo
    owner: Reaction
    domain_of:
    - Reaction
    range: boolean
  is_transport:
    name: is_transport
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: is_transport
    owner: Reaction
    domain_of:
    - Reaction
    range: boolean
  left_participants:
    name: left_participants
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    is_a: has_participants
    domain: Reaction
    multivalued: true
    alias: left_participants
    owner: Reaction
    domain_of:
    - Reaction
    range: ReactionParticipant
  right_participants:
    name: right_participants
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    is_a: has_participants
    domain: Reaction
    multivalued: true
    alias: right_participants
    owner: Reaction
    domain_of:
    - Reaction
    range: ReactionParticipant
  smarts_string:
    name: smarts_string
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: smarts_string
    owner: Reaction
    domain_of:
    - Reaction
    range: string
  id:
    name: id
    description: A unique identifier for a thing. Must be either a CURIE shorthand
      for a URI or a complete URI
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    identifier: true
    alias: id
    owner: Reaction
    domain_of:
    - Biosample
    - Study
    - NamedThing
    - Activity
    range: uriorcurie
    required: true
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
  name:
    name: name
    description: A human readable label for an entity
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: name
    owner: Reaction
    domain_of:
    - Protocol
    - NamedThing
    - PersonValue
    - Activity
    range: string
  description:
    name: description
    description: a human-readable description of a thing
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: dcterms:description
    alias: description
    owner: Reaction
    domain_of:
    - Study
    - NamedThing
    - ImageValue
    range: string
  alternative_identifiers:
    name: alternative_identifiers
    description: A list of alternative identifiers for the entity.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    multivalued: true
    alias: alternative_identifiers
    owner: Reaction
    domain_of:
    - Biosample
    - Study
    - NamedThing
    - MetaboliteQuantification
    range: uriorcurie
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$