Class: Pathway

Curated grouping of biologically related events representing a pathway or pathway-like module.

 classDiagram
    class Pathway
    click Pathway href "../Pathway/"
      Event <|-- Pathway
        click Event href "../Event/"

      Pathway : created





        Pathway --> "1" InstanceEdit : created
        click InstanceEdit href "../InstanceEdit/"



      Pathway : definition

      Pathway : description

      Pathway : display_label

      Pathway : has_cross_reference





        Pathway --> "*" DatabaseIdentifier : has_cross_reference
        click DatabaseIdentifier href "../DatabaseIdentifier/"



      Pathway : has_disease_context





        Pathway --> "*" Disease : has_disease_context
        click Disease href "../Disease/"



      Pathway : has_event





        Pathway --> "1..*" Event : has_event
        click Event href "../Event/"



      Pathway : has_go_biological_process





        Pathway --> "0..1" GoBiologicalProcessTerm : has_go_biological_process
        click GoBiologicalProcessTerm href "../GoBiologicalProcessTerm/"



      Pathway : has_summation





        Pathway --> "0..1" Summation : has_summation
        click Summation href "../Summation/"



      Pathway : id

      Pathway : in_taxon





        Pathway --> "*" OrganismTaxon : in_taxon
        click OrganismTaxon href "../OrganismTaxon/"



      Pathway : is_inferred

      Pathway : located_in_compartment





        Pathway --> "*" Compartment : located_in_compartment
        click Compartment href "../Compartment/"



      Pathway : modified





        Pathway --> "*" InstanceEdit : modified
        click InstanceEdit href "../InstanceEdit/"



      Pathway : name

      Pathway : previous_stable_identifier

      Pathway : reactome_db_id

      Pathway : reactome_stable_identifier

      Pathway : release_date

      Pathway : release_status

      Pathway : reviewed





        Pathway --> "*" InstanceEdit : reviewed
        click InstanceEdit href "../InstanceEdit/"



      Pathway : revised





        Pathway --> "*" InstanceEdit : revised
        click InstanceEdit href "../InstanceEdit/"



      Pathway : source_schema_class

      Pathway : supported_by





        Pathway --> "*" Publication : supported_by
        click Publication href "../Publication/"

Inheritance

NamedEntity
- DatabaseObject
  - Event
    - Pathway

Class Properties

Property	Value
Class URI	reactome:Pathway

Slots

Name	Cardinality and Range	Description	Inheritance
has_event	1..* Event	Membership relation linking a pathway to constituent events	direct
has_go_biological_process	0..1 GoBiologicalProcessTerm	GO biological process term associated with a Reactome pathway or event	direct
in_taxon	* OrganismTaxon	Taxon in which the object, event, or entity is asserted to occur or be define...	Event
located_in_compartment	* Compartment	Compartment in which an entity resides or an event occurs	Event
has_summation	0..1 Summation	Narrative summary object explaining the biology of an event or entity	Event
has_cross_reference	* DatabaseIdentifier	External cross-reference to another database or controlled resource	Event
has_disease_context	* Disease	Disease context associated with an event or physical entity	Event
supported_by	* Publication	Publication supporting the existence, mechanism, or curation of the object	Event
reviewed	* InstanceEdit	Provenance links to formal review actions on the object	Event
revised	* InstanceEdit	Provenance links to explicit revision actions after prior curation or review	Event
release_date	0..1 date	Release date associated with a curation or publication cycle	Event
release_status	0..1 String	Editorial release state of the object in the Reactome release process	Event
is_inferred	0..1 Boolean	Indicates whether an object was computationally inferred rather than directly...	Event
reactome_db_id	1 Integer	Internal Reactome database identifier assigned to a database object	DatabaseObject
reactome_stable_identifier	1 String	Stable public Reactome identifier for an object	DatabaseObject
source_schema_class	1 String	Name of the source Reactome schema class from which the instance derives	DatabaseObject
display_label	1 String	Preferred display label used by Reactome for user-facing presentation	DatabaseObject
definition	0..1 String	Curated textual definition that states what the object is	DatabaseObject
previous_stable_identifier	0..1 String	Deprecated or previous stable Reactome identifier retained for traceability	DatabaseObject
created	1 InstanceEdit	Provenance link to the curation event that originally created the object reco...	DatabaseObject
modified	* InstanceEdit	Provenance links to subsequent modifications of the object record	DatabaseObject
id	1 String	Unique identifier for an instance in the serialized dataset	NamedEntity
name	0..1 String	Human-readable primary label for an object	NamedEntity
description	0..1 String	Free-text textual description of an object	NamedEntity

Comments

Pathways can overlap; event membership is not exclusive.

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/reactome-ontology

Mappings

Mapping Type	Mapped Value
self	reactome:Pathway
native	reactome:Pathway

LinkML Source

Direct

name: pathway
description: Curated grouping of biologically related events representing a pathway
  or pathway-like module.
comments:
- Pathways can overlap; event membership is not exclusive.
from_schema: https://w3id.org/reactome-ontology
is_a: event
slots:
- has_event
- has_go_biological_process
slot_usage:
  has_event:
    name: has_event
    required: true
class_uri: reactome:Pathway

Induced

name: pathway
description: Curated grouping of biologically related events representing a pathway
  or pathway-like module.
comments:
- Pathways can overlap; event membership is not exclusive.
from_schema: https://w3id.org/reactome-ontology
is_a: event
slot_usage:
  has_event:
    name: has_event
    required: true
attributes:
  has_event:
    name: has_event
    description: Membership relation linking a pathway to constituent events.
    comments:
    - Pathways in Reactome are curated groupings of events and can overlap with other
      pathways.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:hasEvent
    alias: has_event
    owner: pathway
    domain_of:
    - pathway
    range: event
    required: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_go_biological_process:
    name: has_go_biological_process
    description: GO biological process term associated with a Reactome pathway or
      event.
    comments:
    - Useful as a high-level semantic alignment rather than an exact equivalence in
      all cases.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:hasGoBiologicalProcess
    alias: has_go_biological_process
    owner: pathway
    domain_of:
    - pathway
    range: go_biological_process_term
    multivalued: false
  in_taxon:
    name: in_taxon
    description: Taxon in which the object, event, or entity is asserted to occur
      or be defined.
    comments:
    - For events this denotes the organism context; for entities it denotes the biological
      source organism.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:inTaxon
    alias: in_taxon
    owner: pathway
    domain_of:
    - event
    - physical_entity
    range: organism_taxon
    multivalued: true
  located_in_compartment:
    name: located_in_compartment
    description: Compartment in which an entity resides or an event occurs.
    comments:
    - In Reactome, compartment is identity-relevant for many physical entities.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:locatedInCompartment
    alias: located_in_compartment
    owner: pathway
    domain_of:
    - event
    - physical_entity
    range: compartment
    multivalued: true
  has_summation:
    name: has_summation
    description: Narrative summary object explaining the biology of an event or entity.
    comments:
    - Distinct from formal definition; usually prose intended for readers.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:hasSummation
    alias: has_summation
    owner: pathway
    domain_of:
    - event
    range: summation
    multivalued: false
  has_cross_reference:
    name: has_cross_reference
    description: External cross-reference to another database or controlled resource.
    comments:
    - Used for interoperating with identifiers from GO, ChEBI, UniProt, Ensembl, and
      related resources.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:hasCrossReference
    alias: has_cross_reference
    owner: pathway
    domain_of:
    - event
    - physical_entity
    range: database_identifier
    multivalued: true
  has_disease_context:
    name: has_disease_context
    description: Disease context associated with an event or physical entity.
    comments:
    - Represents contextual disease association rather than broad etiologic modeling.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:hasDiseaseContext
    alias: has_disease_context
    owner: pathway
    domain_of:
    - event
    - physical_entity
    range: disease
    multivalued: true
  supported_by:
    name: supported_by
    description: Publication supporting the existence, mechanism, or curation of the
      object.
    comments:
    - Often points to PubMed-backed literature references.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:supportedBy
    alias: supported_by
    owner: pathway
    domain_of:
    - event
    - catalyst_activity
    - regulation
    range: publication
    multivalued: true
  reviewed:
    name: reviewed
    description: Provenance links to formal review actions on the object.
    comments:
    - Distinct from simple modification in Reactome curation workflows.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:reviewed
    alias: reviewed
    owner: pathway
    domain_of:
    - event
    range: instance_edit
    multivalued: true
  revised:
    name: revised
    description: Provenance links to explicit revision actions after prior curation
      or review.
    comments:
    - Useful for tracking editorial iteration.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:revised
    alias: revised
    owner: pathway
    domain_of:
    - event
    range: instance_edit
    multivalued: true
  release_date:
    name: release_date
    description: Release date associated with a curation or publication cycle.
    comments:
    - Modeled as string to match Reactome exports; can be normalized later if needed.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:releaseDate
    alias: release_date
    owner: pathway
    domain_of:
    - event
    range: date
    multivalued: false
  release_status:
    name: release_status
    description: Editorial release state of the object in the Reactome release process.
    comments:
    - Examples might include draft-like or released-like status labels depending on
      source exports.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:releaseStatus
    alias: release_status
    owner: pathway
    domain_of:
    - event
    range: string
    multivalued: false
  is_inferred:
    name: is_inferred
    description: Indicates whether an object was computationally inferred rather than
      directly curated.
    comments:
    - Reactome uses inference especially for orthology-based event propagation.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:isInferred
    alias: is_inferred
    owner: pathway
    domain_of:
    - event
    range: boolean
    multivalued: false
  reactome_db_id:
    name: reactome_db_id
    description: Internal Reactome database identifier assigned to a database object.
    comments:
    - Reactome DB_ID values are implementation-oriented identifiers rather than stable
      public identifiers.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:reactomeDbId
    alias: reactome_db_id
    owner: pathway
    domain_of:
    - database_object
    range: integer
    required: true
    multivalued: false
  reactome_stable_identifier:
    name: reactome_stable_identifier
    description: Stable public Reactome identifier for an object.
    comments:
    - Typically corresponds to the curated Reactome stable accession such as R-HSA-xxxxx.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:reactomeStableIdentifier
    alias: reactome_stable_identifier
    owner: pathway
    domain_of:
    - database_object
    range: string
    required: true
    multivalued: false
  source_schema_class:
    name: source_schema_class
    description: Name of the source Reactome schema class from which the instance
      derives.
    comments:
    - Useful when preserving frame-schema provenance or round-tripping with the original
      Reactome graph.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:sourceSchemaClass
    alias: source_schema_class
    owner: pathway
    domain_of:
    - database_object
    range: string
    required: true
    multivalued: false
  display_label:
    name: display_label
    description: Preferred display label used by Reactome for user-facing presentation.
    comments:
    - Often combines identity and contextual state into a concise label.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    is_a: name
    slot_uri: reactome:displayLabel
    alias: display_label
    owner: pathway
    domain_of:
    - database_object
    range: string
    required: true
    multivalued: false
  definition:
    name: definition
    description: Curated textual definition that states what the object is.
    comments:
    - Intended for conceptual definitions rather than narrative summaries.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:definition
    alias: definition
    owner: pathway
    domain_of:
    - database_object
    range: string
    multivalued: false
  previous_stable_identifier:
    name: previous_stable_identifier
    description: Deprecated or previous stable Reactome identifier retained for traceability.
    comments:
    - Useful during migration, identifier replacement, and legacy resolution.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:previousStableIdentifier
    alias: previous_stable_identifier
    owner: pathway
    domain_of:
    - database_object
    range: string
    multivalued: false
  created:
    name: created
    description: Provenance link to the curation event that originally created the
      object record.
    comments:
    - Usually points to an InstanceEdit containing editor and date metadata.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:created
    alias: created
    owner: pathway
    domain_of:
    - database_object
    range: instance_edit
    required: true
    multivalued: false
  modified:
    name: modified
    description: Provenance links to subsequent modifications of the object record.
    comments:
    - Multiple modifications are common across curation history.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:modified
    alias: modified
    owner: pathway
    domain_of:
    - database_object
    range: instance_edit
    multivalued: true
  id:
    name: id
    description: Unique identifier for an instance in the serialized dataset.
    comments:
    - This may be a local identifier, CURIE, URI, or other serialization key.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: dcterms:identifier
    identifier: true
    alias: id
    owner: pathway
    domain_of:
    - named_entity
    range: string
    required: true
  name:
    name: name
    description: Human-readable primary label for an object.
    comments:
    - Generic reusable naming slot for schema-wide use.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: rdfs:label
    alias: name
    owner: pathway
    domain_of:
    - named_entity
    range: string
  description:
    name: description
    description: Free-text textual description of an object.
    comments:
    - Can hold editorial notes, plain-language explanations, or short summaries.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: dcterms:description
    alias: description
    owner: pathway
    domain_of:
    - named_entity
    range: string
    multivalued: false
class_uri: reactome:Pathway