Class: PhysicalEntity

Concrete biological participant whose identity reflects both underlying molecular identity and contextual state.

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

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


      PhysicalEntity <|-- SimpleEntity
        click SimpleEntity href "../SimpleEntity/"
      PhysicalEntity <|-- GenomeEncodedEntity
        click GenomeEncodedEntity href "../GenomeEncodedEntity/"
      PhysicalEntity <|-- Complex
        click Complex href "../Complex/"
      PhysicalEntity <|-- EntitySet
        click EntitySet href "../EntitySet/"
      PhysicalEntity <|-- Polymer
        click Polymer href "../Polymer/"
      PhysicalEntity <|-- Cell
        click Cell href "../Cell/"
      PhysicalEntity <|-- OtherEntity
        click OtherEntity href "../OtherEntity/"
      PhysicalEntity <|-- Drug
        click Drug href "../Drug/"


      PhysicalEntity : created





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



      PhysicalEntity : definition

      PhysicalEntity : description

      PhysicalEntity : display_label

      PhysicalEntity : has_cross_reference





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



      PhysicalEntity : has_disease_context





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



      PhysicalEntity : has_go_cellular_component





        PhysicalEntity --> "0..1" GoCellularComponentTerm : has_go_cellular_component
        click GoCellularComponentTerm href "../GoCellularComponentTerm/"



      PhysicalEntity : id

      PhysicalEntity : in_taxon





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



      PhysicalEntity : is_in_disease_context

      PhysicalEntity : located_in_compartment





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



      PhysicalEntity : modified





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



      PhysicalEntity : name

      PhysicalEntity : previous_stable_identifier

      PhysicalEntity : reactome_db_id

      PhysicalEntity : reactome_stable_identifier

      PhysicalEntity : source_schema_class

      PhysicalEntity : systematic_name

Inheritance

NamedEntity
- DatabaseObject
  - PhysicalEntity
    - SimpleEntity
    - GenomeEncodedEntity
    - Complex
    - EntitySet
    - Polymer
    - Cell
    - OtherEntity
    - Drug

Class Properties

Property	Value
Class URI	reactome:PhysicalEntity

Slots

Name	Cardinality and Range	Description	Inheritance
in_taxon	* OrganismTaxon	Taxon in which the object, event, or entity is asserted to occur or be define...	direct
located_in_compartment	* Compartment	Compartment in which an entity resides or an event occurs	direct
has_cross_reference	* DatabaseIdentifier	External cross-reference to another database or controlled resource	direct
has_disease_context	* Disease	Disease context associated with an event or physical entity	direct
has_go_cellular_component	0..1 GoCellularComponentTerm	GO cellular component term associated with a physical entity or event context	direct
systematic_name	0..1 String	Formal or systematic name for an entity when available	direct
is_in_disease_context	0..1 Boolean	Boolean flag indicating that the represented entity is contextualized to a di...	direct
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
ReactionLikeEvent	has_input	range	PhysicalEntity
ReactionLikeEvent	has_output	range	PhysicalEntity
ReactionLikeEvent	requires_component	range	PhysicalEntity
ReactionLikeEvent	has_interacting_entity_on_other_cell	range	PhysicalEntity
Reaction	has_input	range	PhysicalEntity
Reaction	has_output	range	PhysicalEntity
Reaction	requires_component	range	PhysicalEntity
Reaction	has_interacting_entity_on_other_cell	range	PhysicalEntity
BlackBoxEvent	has_input	range	PhysicalEntity
BlackBoxEvent	has_output	range	PhysicalEntity
BlackBoxEvent	requires_component	range	PhysicalEntity
BlackBoxEvent	has_interacting_entity_on_other_cell	range	PhysicalEntity
Polymerization	has_input	range	PhysicalEntity
Polymerization	has_output	range	PhysicalEntity
Polymerization	requires_component	range	PhysicalEntity
Polymerization	has_interacting_entity_on_other_cell	range	PhysicalEntity
Depolymerization	has_input	range	PhysicalEntity
Depolymerization	has_output	range	PhysicalEntity
Depolymerization	requires_component	range	PhysicalEntity
Depolymerization	has_interacting_entity_on_other_cell	range	PhysicalEntity
Complex	has_component	range	PhysicalEntity
EntitySet	has_member	range	PhysicalEntity
CandidateSet	has_member	range	PhysicalEntity
DefinedSet	has_member	range	PhysicalEntity
Polymer	has_repeated_unit	range	PhysicalEntity
CatalystActivity	has_catalyst	range	PhysicalEntity
CatalystActivity	has_active_unit	range	PhysicalEntity
Regulation	has_regulator	range	PhysicalEntity
Regulation	has_active_unit	range	PhysicalEntity
PositiveRegulation	has_regulator	range	PhysicalEntity
PositiveRegulation	has_active_unit	range	PhysicalEntity
NegativeRegulation	has_regulator	range	PhysicalEntity
NegativeRegulation	has_active_unit	range	PhysicalEntity
Requirement	has_regulator	range	PhysicalEntity
Requirement	has_active_unit	range	PhysicalEntity

Comments

In Reactome, compartment, modification state, and assembly state can distinguish one physical entity from another.

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: physical_entity
description: Concrete biological participant whose identity reflects both underlying
  molecular identity and contextual state.
comments:
- In Reactome, compartment, modification state, and assembly state can distinguish
  one physical entity from another.
from_schema: https://w3id.org/reactome-ontology
is_a: database_object
abstract: true
slots:
- in_taxon
- located_in_compartment
- has_cross_reference
- has_disease_context
- has_go_cellular_component
- systematic_name
- is_in_disease_context
class_uri: reactome:PhysicalEntity

Induced

name: physical_entity
description: Concrete biological participant whose identity reflects both underlying
  molecular identity and contextual state.
comments:
- In Reactome, compartment, modification state, and assembly state can distinguish
  one physical entity from another.
from_schema: https://w3id.org/reactome-ontology
is_a: database_object
abstract: true
attributes:
  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: physical_entity
    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: physical_entity
    domain_of:
    - event
    - physical_entity
    range: compartment
    multivalued: true
  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: physical_entity
    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: physical_entity
    domain_of:
    - event
    - physical_entity
    range: disease
    multivalued: true
  has_go_cellular_component:
    name: has_go_cellular_component
    description: GO cellular component term associated with a physical entity or event
      context.
    comments:
    - Often complements the explicit compartment modeling in Reactome.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:hasGoCellularComponent
    alias: has_go_cellular_component
    owner: physical_entity
    domain_of:
    - physical_entity
    range: go_cellular_component_term
    multivalued: false
  systematic_name:
    name: systematic_name
    description: Formal or systematic name for an entity when available.
    comments:
    - Often useful for chemicals, complexes, or sequence-derived entities.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:systematicName
    alias: systematic_name
    owner: physical_entity
    domain_of:
    - physical_entity
    range: string
    multivalued: false
  is_in_disease_context:
    name: is_in_disease_context
    description: Boolean flag indicating that the represented entity is contextualized
      to a disease state.
    comments:
    - This is a contextual flag and does not by itself define a disease ontology class.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:isInDiseaseContext
    alias: is_in_disease_context
    owner: physical_entity
    domain_of:
    - physical_entity
    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: physical_entity
    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: physical_entity
    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: physical_entity
    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: physical_entity
    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: physical_entity
    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: physical_entity
    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: physical_entity
    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: physical_entity
    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: physical_entity
    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: physical_entity
    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: physical_entity
    domain_of:
    - named_entity
    range: string
    multivalued: false
class_uri: reactome:PhysicalEntity