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Class: DatabaseObject

Root class for most Reactome schema objects and the main provenance-bearing superclass.

URI: reactome:DatabaseObject

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


      DatabaseObject <|-- InstanceEdit
        click InstanceEdit href "../InstanceEdit/"
      DatabaseObject <|-- Publication
        click Publication href "../Publication/"
      DatabaseObject <|-- Person
        click Person href "../Person/"
      DatabaseObject <|-- Summation
        click Summation href "../Summation/"
      DatabaseObject <|-- Event
        click Event href "../Event/"
      DatabaseObject <|-- PhysicalEntity
        click PhysicalEntity href "../PhysicalEntity/"
      DatabaseObject <|-- ReferenceEntity
        click ReferenceEntity href "../ReferenceEntity/"
      DatabaseObject <|-- ReferenceDatabase
        click ReferenceDatabase href "../ReferenceDatabase/"
      DatabaseObject <|-- DatabaseIdentifier
        click DatabaseIdentifier href "../DatabaseIdentifier/"
      DatabaseObject <|-- CatalystActivity
        click CatalystActivity href "../CatalystActivity/"
      DatabaseObject <|-- Regulation
        click Regulation href "../Regulation/"
      DatabaseObject <|-- Interaction
        click Interaction href "../Interaction/"
      DatabaseObject <|-- ReactionTypeTerm
        click ReactionTypeTerm href "../ReactionTypeTerm/"
      DatabaseObject <|-- AbstractModifiedResidue
        click AbstractModifiedResidue href "../AbstractModifiedResidue/"
      DatabaseObject <|-- OrganismTaxon
        click OrganismTaxon href "../OrganismTaxon/"
      DatabaseObject <|-- Taxon
        click Taxon href "../Taxon/"
      DatabaseObject <|-- Compartment
        click Compartment href "../Compartment/"
      DatabaseObject <|-- Disease
        click Disease href "../Disease/"
      DatabaseObject <|-- GoMolecularFunctionTerm
        click GoMolecularFunctionTerm href "../GoMolecularFunctionTerm/"
      DatabaseObject <|-- GoBiologicalProcessTerm
        click GoBiologicalProcessTerm href "../GoBiologicalProcessTerm/"
      DatabaseObject <|-- GoCellularComponentTerm
        click GoCellularComponentTerm href "../GoCellularComponentTerm/"


      DatabaseObject : created





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



      DatabaseObject : definition

      DatabaseObject : description

      DatabaseObject : display_label

      DatabaseObject : id

      DatabaseObject : modified





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



      DatabaseObject : name

      DatabaseObject : previous_stable_identifier

      DatabaseObject : reactome_db_id

      DatabaseObject : reactome_stable_identifier

      DatabaseObject : source_schema_class

Inheritance

Class Properties

Property Value
Class URI reactome:DatabaseObject

Slots

Name Cardinality and Range Description Inheritance
reactome_db_id 1
Integer		 Internal Reactome database identifier assigned to a database object direct
reactome_stable_identifier 1
String		 Stable public Reactome identifier for an object direct
source_schema_class 1
String		 Name of the source Reactome schema class from which the instance derives direct
display_label 1
String		 Preferred display label used by Reactome for user-facing presentation direct
definition 0..1
String		 Curated textual definition that states what the object is direct
previous_stable_identifier 0..1
String		 Deprecated or previous stable Reactome identifier retained for traceability direct
created 1
InstanceEdit		 Provenance link to the curation event that originally created the object reco... direct
modified *
InstanceEdit		 Provenance links to subsequent modifications of the object record direct
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
ReactomeDataset database_objects range DatabaseObject

Comments

  • Reactome’s frame-based model uses DatabaseObject as the common ancestor for curated graph records.

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: database_object
description: Root class for most Reactome schema objects and the main provenance-bearing
  superclass.
comments:
- Reactome’s frame-based model uses DatabaseObject as the common ancestor for curated
  graph records.
from_schema: https://w3id.org/reactome-ontology
is_a: named_entity
slots:
- reactome_db_id
- reactome_stable_identifier
- source_schema_class
- display_label
- definition
- previous_stable_identifier
- created
- modified
slot_usage:
  reactome_db_id:
    name: reactome_db_id
    required: true
  reactome_stable_identifier:
    name: reactome_stable_identifier
    required: true
  source_schema_class:
    name: source_schema_class
    required: true
  display_label:
    name: display_label
    required: true
  created:
    name: created
    required: true
class_uri: reactome:DatabaseObject

Induced

name: database_object
description: Root class for most Reactome schema objects and the main provenance-bearing
  superclass.
comments:
- Reactome’s frame-based model uses DatabaseObject as the common ancestor for curated
  graph records.
from_schema: https://w3id.org/reactome-ontology
is_a: named_entity
slot_usage:
  reactome_db_id:
    name: reactome_db_id
    required: true
  reactome_stable_identifier:
    name: reactome_stable_identifier
    required: true
  source_schema_class:
    name: source_schema_class
    required: true
  display_label:
    name: display_label
    required: true
  created:
    name: created
    required: 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: database_object
    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: database_object
    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: database_object
    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: database_object
    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: database_object
    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: database_object
    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: database_object
    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: database_object
    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: database_object
    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: database_object
    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: database_object
    domain_of:
    - named_entity
    range: string
    multivalued: false
class_uri: reactome:DatabaseObject