Class: Publication

Publication record used as evidence or supporting documentation for curated biology.

NOTE: this is an abstract class and should not be instantiated directly

 classDiagram
    class Publication
    click Publication href "../Publication/"
      DatabaseObject <|-- Publication
        click DatabaseObject href "../DatabaseObject/"


      Publication <|-- LiteratureReference
        click LiteratureReference href "../LiteratureReference/"


      Publication : created





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



      Publication : definition

      Publication : description

      Publication : display_label

      Publication : id

      Publication : modified





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



      Publication : name

      Publication : previous_stable_identifier

      Publication : reactome_db_id

      Publication : reactome_stable_identifier

      Publication : source_schema_class

Inheritance

NamedEntity
- DatabaseObject
  - Publication
    - LiteratureReference

Class Properties

Property	Value
Class URI	reactome:Publication

Slots

Name	Cardinality and Range	Description	Inheritance
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

Usages

used by	used in	type	used
Event	supported_by	range	Publication
Pathway	supported_by	range	Publication
ReactionLikeEvent	supported_by	range	Publication
Reaction	supported_by	range	Publication
BlackBoxEvent	supported_by	range	Publication
Polymerization	supported_by	range	Publication
Depolymerization	supported_by	range	Publication
CatalystActivity	supported_by	range	Publication
Regulation	supported_by	range	Publication
PositiveRegulation	supported_by	range	Publication
NegativeRegulation	supported_by	range	Publication
Requirement	supported_by	range	Publication

Comments

Abstract superclass for specific publication-like records.

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: publication
description: Publication record used as evidence or supporting documentation for curated
  biology.
comments:
- Abstract superclass for specific publication-like records.
from_schema: https://w3id.org/reactome-ontology
is_a: database_object
abstract: true
class_uri: reactome:Publication

Induced

name: publication
description: Publication record used as evidence or supporting documentation for curated
  biology.
comments:
- Abstract superclass for specific publication-like records.
from_schema: https://w3id.org/reactome-ontology
is_a: database_object
abstract: true
attributes:
  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: publication
    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: publication
    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: publication
    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: publication
    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: publication
    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: publication
    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: publication
    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: publication
    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: publication
    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: publication
    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: publication
    domain_of:
    - named_entity
    range: string
    multivalued: false
class_uri: reactome:Publication