reactome_ontology
type: Ontology
license: https://creativecommons.org/licenses/by/4.0/
title: Reactome Ontology Model
version: 1.0.0
definition: An OWL-oriented LinkML schema for generating a clean Reactome ontology. This profile keeps ontology-facing classes and properties and removes source-mapping annotations, which are maintained in separate mapping files.
note: Administrative and serialization helper fields are retained for round-tripping but may be omitted from OWL export profiles.
note: Inverse-style helper relations have been removed from the ontology-facing profile in favor of canonical relations.
note: This schema favors ontology-oriented naming for OWL generation; source mappings are maintained in separate mapping files.

reactome_dataset
type: Class
subclass of: Restriction
  min cardinality: 0
  on property: database_objects
subclass of: Restriction
  all values from: database_object
  on property: database_objects
definition: Top-level container for a serialized Reactome dataset excerpt or export package.
in scheme: reactome-ontology
note: Provides a practical root object for JSON and YAML instance data.

authored
type: ObjectProperty
range: instance_edit
definition: Provenance links capturing authoring actions for the object.
in scheme: reactome-ontology
note: Included to support richer editorial provenance when present in exports.

category
type: DatatypeProperty
range: string
definition: Explicit category designator used in serialized instances.
in scheme: reactome-ontology
note: Useful when data are exchanged in JSON or YAML and class typing must be preserved.

black_box_event
type: Class
subclass of: reaction_like_event
definition: Reaction-like event included in the pathway model despite incomplete mechanistic detail.
in scheme: reactome-ontology
note: Useful when biological evidence supports the event but not a full molecular mechanism.

candidate_set
type: Class
subclass of: entity_set
definition: Entity set whose members are candidates for fulfilling a shared biological role.
in scheme: reactome-ontology
note: Often reflects partial knowledge or broad functional grouping.

cell
type: Class
subclass of: physical_entity
definition: Cell or cell-like biological unit treated as a physical participant in an event.
in scheme: reactome-ontology
note: Included for cases where cells themselves are modeled as interacting biological entities.

chemical_drug
type: Class
subclass of: drug
definition: Drug represented primarily as a chemical or small-molecule therapeutic agent.
in scheme: reactome-ontology
note: Often alignable to small-molecule reference identities.

complex
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: has_component
subclass of: Restriction
  all values from: physical_entity
  on property: has_component
subclass of: physical_entity
definition: Physical entity composed of two or more component physical entities assembled into a functional complex.
in scheme: reactome-ontology
note: The complex is treated as an entity distinct from its components.

defined_set
type: Class
subclass of: entity_set
definition: Entity set whose members are explicitly curated as the intended interchangeable participants.
in scheme: reactome-ontology
note: Stronger editorial commitment than a candidate set.

depolymerization
type: Class
subclass of: reaction_like_event
definition: Event representing breakdown of a polymer into constituent or smaller units.
in scheme: reactome-ontology
note: Complementary to polymerisation.

literature_reference
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: pubmed_id
subclass of: Restriction
  all values from: Datatype
    intersection of: string
    intersection of: Datatype
      on datatype: string
      with restrictions:
        pattern: ^[0-9]+$
  on property: pubmed_id
subclass of: Restriction
  min cardinality: 0
  on property: pubmed_id
subclass of: publication
definition: Literature citation record, commonly representing a PubMed-indexed paper supporting a Reactome assertion.
in scheme: reactome-ontology
note: Used widely to ground events, regulations, and catalyst activities in the literature.

negative_regulation
type: Class
subclass of: regulation
definition: Regulation that decreases, inhibits, or negatively influences the occurrence or efficiency of a reaction-like event.
in scheme: reactome-ontology
note: Semantic polarity is explicit at the class level.

other_entity
type: Class
subclass of: physical_entity
definition: Catch-all physical entity class for biologically relevant participants not covered by more specific subclasses.
in scheme: reactome-ontology
note: Helps preserve source fidelity when Reactome uses residual categorization.

pathway
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: has_go_biological_process
subclass of: Restriction
  all values from: event
  on property: has_event
subclass of: Restriction
  min cardinality: 0
  on property: has_go_biological_process
subclass of: Restriction
  all values from: go_biological_process_term
  on property: has_go_biological_process
subclass of: Restriction
  min cardinality: 1
  on property: has_event
subclass of: event
definition: Curated grouping of biologically related events representing a pathway or pathway-like module.
in scheme: reactome-ontology
note: Pathways can overlap; event membership is not exclusive.

polymer
type: Class
subclass of: Restriction
  min cardinality: 0
  on property: has_repeated_unit
subclass of: Restriction
  all values from: physical_entity
  on property: has_repeated_unit
subclass of: physical_entity
definition: Polymer entity abstracted in terms of one or more repeated units.
in scheme: reactome-ontology
note: Useful for biological polymers that are not modeled by enumerating every monomer instance.

polymerization
type: Class
subclass of: reaction_like_event
definition: Event representing formation of a polymer from repeated or assembling units.
in scheme: reactome-ontology
note: Kept distinct because its participant semantics can differ from ordinary reaction balance.

positive_regulation
type: Class
subclass of: regulation
definition: Regulation that increases, enables, or positively influences the occurrence or efficiency of a reaction-like event.
in scheme: reactome-ontology
note: Semantic polarity is explicit at the class level.

protein_drug
type: Class
subclass of: drug
definition: Drug represented as a protein therapeutic or protein-derived biologic.
in scheme: reactome-ontology
note: Includes antibody-like or recombinant protein therapeutics when modeled as physical entities.

reaction
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: has_input
subclass of: Restriction
  min cardinality: 1
  on property: has_output
subclass of: Restriction
  all values from: physical_entity
  on property: has_output
subclass of: Restriction
  all values from: physical_entity
  on property: has_input
subclass of: reaction_like_event
definition: Standard reaction-like event with explicit transformed inputs and outputs.
in scheme: reactome-ontology
note: Best used for relatively well-resolved mechanistic conversions.

reference_dna_sequence
type: Class
subclass of: reference_sequence
definition: Reference identity for a DNA sequence.
in scheme: reactome-ontology
note: Supports DNA-centric entities in the Reactome schema.

reference_gene_product
type: Class
subclass of: reference_sequence
definition: Reference sequence corresponding to a gene product, typically protein-centric.
in scheme: reactome-ontology
note: Often alignable to UniProt entries for proteins.

reference_group
type: Class
subclass of: reference_entity
definition: Grouped reference identity used when an invariant identity is represented at a grouped rather than single-entry level.
in scheme: reactome-ontology
note: Useful for families or grouped reference semantics in source data.

reference_isoform
type: Class
subclass of: reference_sequence
definition: Reference sequence representing a specific isoform-level identity.
in scheme: reactome-ontology
note: Useful when isoform distinction matters biologically.

reference_rna_sequence
type: Class
subclass of: reference_sequence
definition: Reference identity for an RNA sequence.
in scheme: reactome-ontology
note: Supports transcript and RNA molecule identity modeling.

reference_therapeutic
type: Class
subclass of: reference_entity
definition: Reference identity for a therapeutic or intervention-oriented entity.
in scheme: reactome-ontology
note: Supports the reference-layer counterpart of drug-like modeled entities.

requirement
type: Class
subclass of: regulation
definition: Regulation-like assertion indicating that a regulator or participant is required for a reaction-like event to occur.
in scheme: reactome-ontology
note: Used when necessity is the key biological relation rather than positive or negative modulation.

rna_drug
type: Class
subclass of: drug
definition: Drug represented as an RNA-based therapeutic agent.
in scheme: reactome-ontology
note: Can cover antisense, siRNA, or related RNA therapeutic modalities.

sequence_entity
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: start_coordinate
subclass of: Restriction
  min cardinality: 0
  on property: start_coordinate
subclass of: Restriction
  max cardinality: 1
  on property: sequence_reference_type
subclass of: Restriction
  max cardinality: 1
  on property: has_reference_entity
subclass of: Restriction
  all values from: abstract_modified_residue
  on property: has_modified_residue
subclass of: Restriction
  max cardinality: 1
  on property: end_coordinate
subclass of: Restriction
  all values from: string
  on property: sequence_reference_type
subclass of: Restriction
  all values from: integer
  on property: end_coordinate
subclass of: Restriction
  min cardinality: 0
  on property: end_coordinate
subclass of: Restriction
  all values from: integer
  on property: start_coordinate
subclass of: Restriction
  min cardinality: 1
  on property: has_reference_entity
subclass of: Restriction
  min cardinality: 0
  on property: sequence_reference_type
subclass of: Restriction
  min cardinality: 0
  on property: has_modified_residue
subclass of: Restriction
  all values from: reference_sequence
  on property: has_reference_entity
subclass of: genome_encoded_entity
definition: Sequence-bearing physical entity linked to a stable reference sequence and optionally decorated with residue modifications and subsequence coordinates.
in scheme: reactome-ontology
note: Core Reactome pattern for proteins, RNAs, and other accessioned biomolecules in specific states.

simple_entity
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: has_reference_entity
subclass of: Restriction
  all values from: reference_molecule
  on property: has_reference_entity
subclass of: Restriction
  min cardinality: 1
  on property: has_reference_entity
subclass of: physical_entity
definition: Simple molecular entity, typically a small molecule or other non-sequence-based chemical participant.
in scheme: reactome-ontology
note: Commonly aligned to ChEBI-like reference identities through ReferenceMolecule.

taxon
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: ncbi_taxon_id
subclass of: Restriction
  all values from: Datatype
    intersection of: string
    intersection of: Datatype
      on datatype: string
      with restrictions:
        pattern: ^[0-9]+$
  on property: ncbi_taxon_id
subclass of: Restriction
  min cardinality: 0
  on property: ncbi_taxon_id
subclass of: database_object
definition: Taxonomic concept used for taxonomic assignment or metadata.
in scheme: reactome-ontology
note: Can be used in parallel with or beneath species-oriented records.

genome_encoded_entity
type: Class
subclass of: physical_entity
definition: Physical entity whose existence is grounded in a genome-encoded product such as a protein or nucleic acid.
in scheme: reactome-ontology
note: Serves as a superclass for accessioned sequence-based entities.

named_entity
type: Class
subclass of: Restriction
  all values from: string
  on property: description
subclass of: Restriction
  all values from: string
  on property: name
subclass of: Restriction
  max cardinality: 1
  on property: id
subclass of: Restriction
  all values from: string
  on property: id
subclass of: Restriction
  min cardinality: 0
  on property: name
subclass of: Restriction
  min cardinality: 1
  on property: id
subclass of: Restriction
  max cardinality: 1
  on property: name
subclass of: Restriction
  min cardinality: 0
  on property: description
subclass of: Restriction
  max cardinality: 1
  on property: description
definition: Generic named entity used as a lightweight semantic root for serializable objects.
in scheme: reactome-ontology
note: Provides reusable identifier, naming, and descriptive slots independent of the Reactome-specific hierarchy.

person
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: orcid
subclass of: Restriction
  min cardinality: 0
  on property: orcid
subclass of: Restriction
  all values from: anyURI
  on property: orcid
subclass of: database_object
definition: Person record used primarily for provenance, authorship, and curation attribution.
in scheme: reactome-ontology
note: May represent curators, reviewers, or contributors.

reference_molecule
type: Class
subclass of: reference_entity
definition: Reference identity for a small molecule, simple chemical, or chemically grounded participant.
in scheme: reactome-ontology
note: Naturally alignable to ChEBI-like references.

author
type: ObjectProperty
definition: Person or people responsible for the edit activity.
in scheme: reactome-ontology

catalyzes
type: ObjectProperty
range: reaction_like_event
definition: Reaction-like event catalyzed by the given catalyst activity.
in scheme: reactome-ontology
note: Allows one catalyst activity node to connect molecular function and event participation.

database_objects
type: ObjectProperty
definition: Collection of Reactome objects keyed by identifier.
in scheme: reactome-ontology

has_catalyst_activity
type: ObjectProperty
range: catalyst_activity
definition: Catalyst activity associated with the reaction-like event.
in scheme: reactome-ontology
note: A central Reactome modeling pattern that preserves GO molecular function and active-unit context.

has_component
type: ObjectProperty
range: physical_entity
definition: Component physical entities that make up a complex.
in scheme: reactome-ontology
note: Complex identity is distinct from component identity in Reactome.

has_event
type: ObjectProperty
range: event
definition: Membership relation linking a pathway to constituent events.
in scheme: reactome-ontology
note: Pathways in Reactome are curated groupings of events and can overlap with other pathways.

has_interacting_entity_on_other_cell
type: ObjectProperty
range: physical_entity
definition: Physical entity located on another interacting cell in intercellular biology.
in scheme: reactome-ontology
note: Useful for immune, adhesion, and receptor-ligand interaction contexts.

has_interaction
type: ObjectProperty
range: interaction
definition: Associated interaction object linked to an event.
in scheme: reactome-ontology
note: Preserves interaction-level detail when Reactome models such assertions explicitly.

has_member
type: ObjectProperty
range: physical_entity
definition: Members of an entity set representing functionally interchangeable participants.
in scheme: reactome-ontology
note: Entity sets are curated graph objects, not simply OWL classes over their members.

has_modified_residue
type: ObjectProperty
range: abstract_modified_residue
definition: Modified residue feature borne by a sequence-based physical entity.
in scheme: reactome-ontology
note: Supports phosphorylation, cleavage, ubiquitination, and related residue-level state modeling.

has_reaction_type
type: ObjectProperty
range: reaction_type_term
definition: Controlled reaction type annotation describing the mechanistic or editorial type of a reaction.
in scheme: reactome-ontology
note: Useful for grouping reaction-like events into broad mechanistic categories.

has_regulation
type: ObjectProperty
range: regulation
definition: Reified regulation assertion attached to an event.
in scheme: reactome-ontology
note: Supports positive, negative, and requirement-style regulatory semantics.

has_repeated_unit
type: ObjectProperty
range: physical_entity
definition: Repeated unit composing a polymer entity.
in scheme: reactome-ontology
note: Used when Reactome models a polymer abstractly in terms of repeating constituents.

modified
type: ObjectProperty
range: instance_edit
definition: Provenance links to subsequent modifications of the object record.
in scheme: reactome-ontology
note: Multiple modifications are common across curation history.

preceded_by
type: ObjectProperty
range: event
definition: Event that occurs before the current event in a curated process sequence.
in scheme: reactome-ontology
note: Encodes partial ordering rather than necessarily strict temporal or causal completeness.

requires_component
type: ObjectProperty
range: physical_entity
definition: Physical entity required for a reaction-like event but not modeled as a transforming input.
in scheme: reactome-ontology
note: Useful for contextual cofactors, platform components, or required participants.

reviewed
type: ObjectProperty
range: instance_edit
definition: Provenance links to formal review actions on the object.
in scheme: reactome-ontology
note: Distinct from simple modification in Reactome curation workflows.

revised
type: ObjectProperty
range: instance_edit
definition: Provenance links to explicit revision actions after prior curation or review.
in scheme: reactome-ontology
note: Useful for tracking editorial iteration.

abstract_modified_residue
type: Class
subclass of: database_object
definition: Feature record describing a modified residue or residue-level state on a sequence-bearing entity.
in scheme: reactome-ontology
note: Abstract superclass for phosphorylation-like or other residue modification records.

catalyst_activity
type: Class
subclass of: Restriction
  all values from: reaction_like_event
  on property: catalyzes
subclass of: Restriction
  min cardinality: 0
  on property: supported_by
subclass of: Restriction
  all values from: physical_entity
  on property: has_active_unit
subclass of: Restriction
  all values from: publication
  on property: supported_by
subclass of: Restriction
  min cardinality: 0
  on property: has_active_unit
subclass of: Restriction
  all values from: physical_entity
  on property: has_catalyst
subclass of: Restriction
  all values from: go_molecular_function_term
  on property: has_go_molecular_function
subclass of: Restriction
  max cardinality: 1
  on property: has_catalyst
subclass of: Restriction
  max cardinality: 1
  on property: has_go_molecular_function
subclass of: Restriction
  min cardinality: 1
  on property: has_catalyst
subclass of: Restriction
  min cardinality: 1
  on property: has_go_molecular_function
subclass of: Restriction
  min cardinality: 0
  on property: catalyzes
subclass of: database_object
definition: Reified catalytic assertion connecting a catalyst bearer, a GO molecular function, and one or more catalyzed reaction-like events.
in scheme: reactome-ontology
note: This is one of the most semantically important reified node types in Reactome.

entity_set
type: Class
subclass of: Restriction
  all values from: physical_entity
  on property: has_member
subclass of: Restriction
  min cardinality: 1
  on property: has_member
subclass of: physical_entity
definition: Curated set of physical entities that are treated as functionally interchangeable in a given biological context.
in scheme: reactome-ontology
note: This is a graph object representing a curated set, not merely a class extension over its members.

go_biological_process_term
type: Class
subclass of: database_object
definition: Wrapper object for a GO biological process term used for pathway or event alignment.
in scheme: reactome-ontology
note: Useful for crosswalks between Reactome pathways and GO process knowledge.

go_cellular_component_term
type: Class
subclass of: database_object
definition: Wrapper object for a GO cellular component term used in entity or location annotation.
in scheme: reactome-ontology
note: Often complements explicit compartment modeling.

go_molecular_function_term
type: Class
subclass of: database_object
definition: Wrapper object for a GO molecular function term used in Reactome catalysis modeling.
in scheme: reactome-ontology
note: Particularly important in CatalystActivity.

interaction
type: Class
subclass of: database_object
definition: Interaction record associated with an event or set of participants.
in scheme: reactome-ontology
note: Retained as a distinct object to preserve graph fidelity when interactions are explicitly modeled.

reaction_type_term
type: Class
subclass of: database_object
definition: Controlled vocabulary term used to characterize a reaction-like event.
in scheme: reactome-ontology
note: Supports editorial or mechanistic grouping of reaction events.

summation
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: text
subclass of: Restriction
  all values from: string
  on property: text
subclass of: Restriction
  max cardinality: 1
  on property: text
subclass of: database_object
definition: Narrative summary record containing prose that explains the biological meaning of an entity or event.
in scheme: reactome-ontology
note: Distinct from a formal definition; meant for human reading.

access_url
type: DatatypeProperty
range: anyURI
definition: URL template or access URL used to resolve an identifier in a reference database.
in scheme: reactome-ontology
note: Can encode direct or templated resolver behavior.

created
type: ObjectProperty
range: instance_edit
definition: Provenance link to the curation event that originally created the object record.
in scheme: reactome-ontology
note: Usually points to an InstanceEdit containing editor and date metadata.

date
type: DatatypeProperty
definition: Timestamp or date string for the edit activity.
in scheme: reactome-ontology

definition
type: DatatypeProperty
range: string
definition: Curated textual definition that states what the object is.
in scheme: reactome-ontology
note: Intended for conceptual definitions rather than narrative summaries.

description
type: DatatypeProperty
range: string
definition: Free-text textual description of an object.
in scheme: reactome-ontology
note: Can hold editorial notes, plain-language explanations, or short summaries.

display_label
type: DatatypeProperty
range: string
sub property of: name
definition: Preferred display label used by Reactome for user-facing presentation.
in scheme: reactome-ontology
note: Often combines identity and contextual state into a concise label.

end_coordinate
type: DatatypeProperty
range: integer
definition: End coordinate of a subsequence, fragment, or feature-bearing region on a sequence entity.
in scheme: reactome-ontology
note: Typically paired with start_coordinate.

has_catalyst
type: ObjectProperty
range: physical_entity
definition: Physical entity serving as the bearer of a catalyst activity.
in scheme: reactome-ontology
note: Used inside reified catalyst activity objects.

has_go_biological_process
type: ObjectProperty
range: go_biological_process_term
definition: GO biological process term associated with a Reactome pathway or event.
in scheme: reactome-ontology
note: Useful as a high-level semantic alignment rather than an exact equivalence in all cases.

has_go_cellular_component
type: ObjectProperty
range: go_cellular_component_term
definition: GO cellular component term associated with a physical entity or event context.
in scheme: reactome-ontology
note: Often complements the explicit compartment modeling in Reactome.

has_go_molecular_function
type: ObjectProperty
range: go_molecular_function_term
definition: GO molecular function term asserted in a catalyst activity.
in scheme: reactome-ontology
note: Reactome reifies catalysis so the molecular function can be attached explicitly.

has_regulator
type: ObjectProperty
range: physical_entity
definition: Physical entity that exerts regulatory influence on a regulated event.
in scheme: reactome-ontology
note: May be a protein, complex, small molecule, set, or other physical entity.

has_summation
type: ObjectProperty
range: summation
definition: Narrative summary object explaining the biology of an event or entity.
in scheme: reactome-ontology
note: Distinct from formal definition; usually prose intended for readers.

id
type: DatatypeProperty
range: string
definition: Unique identifier for an instance in the serialized dataset.
in scheme: reactome-ontology
note: This may be a local identifier, CURIE, URI, or other serialization key.

identifier_prefix
type: DatatypeProperty
range: string
definition: Prefix or namespace abbreviation used by a reference database.
in scheme: reactome-ontology
note: Useful for CURIE generation and namespace harmonization.

is_in_disease_context
type: DatatypeProperty
range: boolean
definition: Boolean flag indicating that the represented entity is contextualized to a disease state.
in scheme: reactome-ontology
note: This is a contextual flag and does not by itself define a disease ontology class.

is_inferred
type: DatatypeProperty
range: boolean
definition: Indicates whether an object was computationally inferred rather than directly curated.
in scheme: reactome-ontology
note: Reactome uses inference especially for orthology-based event propagation.

orcid
type: DatatypeProperty
range: anyURI
definition: ORCID identifier for a person involved in curation or authorship.
in scheme: reactome-ontology
note: Useful for curator and contributor disambiguation.

previous_stable_identifier
type: DatatypeProperty
range: string
definition: Deprecated or previous stable Reactome identifier retained for traceability.
in scheme: reactome-ontology
note: Useful during migration, identifier replacement, and legacy resolution.

pubmed_id
type: DatatypeProperty
range: Datatype
  intersection of: string
  intersection of: Datatype
    on datatype: string
    with restrictions:
      pattern: ^[0-9]+$
definition: PubMed identifier for a literature reference.
in scheme: reactome-ontology
note: Stored as string for broad interoperability with exports and loaders.

reactome_db_id
type: DatatypeProperty
range: integer
definition: Internal Reactome database identifier assigned to a database object.
in scheme: reactome-ontology
note: Reactome DB_ID values are implementation-oriented identifiers rather than stable public identifiers.

reactome_stable_identifier
type: DatatypeProperty
range: string
definition: Stable public Reactome identifier for an object.
in scheme: reactome-ontology
note: Typically corresponds to the curated Reactome stable accession such as R-HSA-xxxxx.

regulates
type: ObjectProperty
range: reaction_like_event
definition: Reaction-like event that is the target of regulation.
in scheme: reactome-ontology
note: Kept explicit through reified regulation nodes rather than flattened triples.

release_date
type: DatatypeProperty
range: date
definition: Release date associated with a curation or publication cycle.
in scheme: reactome-ontology
note: Modeled as string to match Reactome exports; can be normalized later if needed.

release_status
type: DatatypeProperty
range: string
definition: Editorial release state of the object in the Reactome release process.
in scheme: reactome-ontology
note: Examples might include draft-like or released-like status labels depending on source exports.

resource_identifier
type: DatatypeProperty
range: string
definition: Identifier for the reference resource itself rather than for entries inside it.
in scheme: reactome-ontology
note: Supports metadata about the authority record for a database.

sequence_reference_type
type: DatatypeProperty
range: string
definition: Textual qualifier for the kind of referenced sequence or entity.
in scheme: reactome-ontology
note: Included for compatibility with Reactome exports.

source_schema_class
type: DatatypeProperty
range: string
definition: Name of the source Reactome schema class from which the instance derives.
in scheme: reactome-ontology
note: Useful when preserving frame-schema provenance or round-tripping with the original Reactome graph.

start_coordinate
type: DatatypeProperty
range: integer
definition: Start coordinate of a subsequence, fragment, or feature-bearing region on a sequence entity.
in scheme: reactome-ontology
note: Useful for proteolytic fragments, domains, and sequence-trimmed entity forms.

systematic_name
type: DatatypeProperty
range: string
definition: Formal or systematic name for an entity when available.
in scheme: reactome-ontology
note: Often useful for chemicals, complexes, or sequence-derived entities.

text
type: DatatypeProperty
definition: Narrative summary text.
in scheme: reactome-ontology

url
type: DatatypeProperty
range: anyURI
definition: General URL associated with an object.
in scheme: reactome-ontology
note: Often used for resource metadata pages or resolver entry points.

compartment
type: Class
subclass of: database_object
definition: Cellular or subcellular location object used to state where an event occurs or where a physical entity resides.
in scheme: reactome-ontology
note: Often alignable to GO cellular component terms, though not always identical in role.

database_identifier
type: Class
subclass of: Restriction
  all values from: reference_database
  on property: has_reference_database
subclass of: Restriction
  max cardinality: 1
  on property: has_reference_database
subclass of: Restriction
  max cardinality: 1
  on property: identifier
subclass of: Restriction
  min cardinality: 0
  on property: identifier
subclass of: Restriction
  all values from: string
  on property: identifier
subclass of: Restriction
  min cardinality: 0
  on property: has_reference_database
subclass of: database_object
definition: Cross-reference record that pairs an identifier string with a reference database authority.
in scheme: reactome-ontology
note: Useful as a reified identifier object rather than a bare literal.

disease
type: Class
subclass of: database_object
definition: Disease concept used to contextualize events and entities in pathological settings.
in scheme: reactome-ontology
note: Represents disease context rather than a full disease ontology commitment.

drug
type: Class
subclass of: physical_entity
definition: Therapeutic or intervention-oriented physical entity modeled in the Reactome graph.
in scheme: reactome-ontology
note: Drug subclasses distinguish broad molecular kinds of therapeutic agents.

organism_taxon
type: Class
subclass of: Restriction
  min cardinality: 0
  on property: ncbi_taxon_id
subclass of: Restriction
  max cardinality: 1
  on property: ncbi_taxon_id
subclass of: Restriction
  all values from: Datatype
    intersection of: string
    intersection of: Datatype
      on datatype: string
      with restrictions:
        pattern: ^[0-9]+$
  on property: ncbi_taxon_id
subclass of: database_object
definition: Organism taxon record representing the organismal context for entities and events.
in scheme: reactome-ontology
note: Often associated with taxonomy identifiers and may correspond to NCBI Taxonomy concepts.

reference_database
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: identifier_prefix
subclass of: Restriction
  all values from: string
  on property: identifier_prefix
subclass of: Restriction
  all values from: anyURI
  on property: url
subclass of: Restriction
  max cardinality: 1
  on property: resource_identifier
subclass of: Restriction
  min cardinality: 0
  on property: url
subclass of: Restriction
  max cardinality: 1
  on property: access_url
subclass of: Restriction
  all values from: anyURI
  on property: access_url
subclass of: Restriction
  min cardinality: 0
  on property: access_url
subclass of: Restriction
  all values from: string
  on property: resource_identifier
subclass of: Restriction
  min cardinality: 0
  on property: identifier_prefix
subclass of: Restriction
  max cardinality: 1
  on property: url
subclass of: Restriction
  min cardinality: 0
  on property: resource_identifier
subclass of: database_object
definition: Metadata record describing an external database or authority used for identifiers and cross-references.
in scheme: reactome-ontology
note: Holds resolver and namespace information for identifier interpretation.

has_active_unit
type: ObjectProperty
range: physical_entity
definition: Subunit, domain-bearing fragment, or active molecular portion responsible for catalytic or regulatory activity.
in scheme: reactome-ontology
note: Reactome can attach active-unit detail to catalyst activities and regulation objects.

has_cross_reference
type: ObjectProperty
range: database_identifier
definition: External cross-reference to another database or controlled resource.
in scheme: reactome-ontology
note: Used for interoperating with identifiers from GO, ChEBI, UniProt, Ensembl, and related resources.

has_disease_context
type: ObjectProperty
range: disease
definition: Disease context associated with an event or physical entity.
in scheme: reactome-ontology
note: Represents contextual disease association rather than broad etiologic modeling.

has_input
type: ObjectProperty
range: physical_entity
definition: Physical entity consumed, transformed, or otherwise used as an input to a reaction-like event.
in scheme: reactome-ontology
note: Inputs need not always be fully consumed in a strict stoichiometric sense across all event subclasses.

has_output
type: ObjectProperty
range: physical_entity
definition: Physical entity produced by a reaction-like event.
in scheme: reactome-ontology
note: Output identity often reflects new compartment, modification state, or assembly state.

in_taxon
type: ObjectProperty
range: organism_taxon
definition: Taxon in which the object, event, or entity is asserted to occur or be defined.
in scheme: reactome-ontology
note: For events this denotes the organism context; for entities it denotes the biological source organism.

located_in_compartment
type: ObjectProperty
range: compartment
definition: Compartment in which an entity resides or an event occurs.
in scheme: reactome-ontology
note: In Reactome, compartment is identity-relevant for many physical entities.

name
type: DatatypeProperty
range: string
definition: Human-readable primary label for an object.
in scheme: reactome-ontology
note: Generic reusable naming slot for schema-wide use.

publication
type: Class
subclass of: database_object
definition: Publication record used as evidence or supporting documentation for curated biology.
in scheme: reactome-ontology
note: Abstract superclass for specific publication-like records.

reference_entity
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: has_reference_database
subclass of: Restriction
  all values from: string
  on property: identifier
subclass of: Restriction
  all values from: reference_database
  on property: has_reference_database
subclass of: Restriction
  min cardinality: 1
  on property: has_reference_database
subclass of: Restriction
  min cardinality: 0
  on property: identifier
subclass of: Restriction
  max cardinality: 1
  on property: identifier
subclass of: database_object
definition: Invariant reference identity used to connect multiple contextualized physical entities that share an underlying molecular identity.
in scheme: reactome-ontology
note: This is the key abstraction Reactome uses to separate contextual state from canonical identity.

reference_sequence
type: Class
subclass of: reference_entity
definition: Reference identity for a sequence-bearing biomolecule.
in scheme: reactome-ontology
note: Commonly used for protein, DNA, RNA, and isoform references.

regulation
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: regulates
subclass of: Restriction
  all values from: reaction_like_event
  on property: regulates
subclass of: Restriction
  all values from: publication
  on property: supported_by
subclass of: Restriction
  max cardinality: 1
  on property: has_regulator
subclass of: Restriction
  all values from: physical_entity
  on property: has_regulator
subclass of: Restriction
  min cardinality: 0
  on property: has_active_unit
subclass of: Restriction
  min cardinality: 1
  on property: regulates
subclass of: Restriction
  min cardinality: 0
  on property: supported_by
subclass of: Restriction
  min cardinality: 1
  on property: has_regulator
subclass of: Restriction
  all values from: physical_entity
  on property: has_active_unit
subclass of: database_object
definition: Reified regulatory assertion linking a regulator physical entity to a regulated reaction-like event.
in scheme: reactome-ontology
note: Reactome models regulation explicitly instead of flattening it into a simple binary relation.

has_reference_database
type: ObjectProperty
range: reference_database
definition: Reference database authority associated with a reference entity or database identifier.
in scheme: reactome-ontology
note: Provides the namespace and interpretation context for an identifier.

has_reference_entity
type: ObjectProperty
range: reference_entity
definition: Invariant reference identity underlying a contextualized physical entity.
in scheme: reactome-ontology
note: {'One of the key distinctions in Reactome': 'reference identity is separate from stateful physical instantiation.'}

identifier
type: DatatypeProperty
range: string
definition: Identifier string assigned by an external reference database.
in scheme: reactome-ontology
note: Examples include UniProt accessions, ChEBI identifiers, or GO term identifiers.

ncbi_taxon_id
type: DatatypeProperty
range: Datatype
  intersection of: string
  intersection of: Datatype
    on datatype: string
    with restrictions:
      pattern: ^[0-9]+$
definition: Taxonomic identifier, typically aligned to the NCBI Taxonomy.
in scheme: reactome-ontology
note: Often used on species or taxon-like records.

supported_by
type: ObjectProperty
range: publication
definition: Publication supporting the existence, mechanism, or curation of the object.
in scheme: reactome-ontology
note: Often points to PubMed-backed literature references.

event
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: release_status
subclass of: Restriction
  all values from: instance_edit
  on property: reviewed
subclass of: Restriction
  min cardinality: 0
  on property: is_inferred
subclass of: Restriction
  all values from: organism_taxon
  on property: in_taxon
subclass of: Restriction
  min cardinality: 0
  on property: has_summation
subclass of: Restriction
  min cardinality: 0
  on property: revised
subclass of: Restriction
  max cardinality: 1
  on property: has_summation
subclass of: Restriction
  min cardinality: 0
  on property: has_cross_reference
subclass of: Restriction
  all values from: instance_edit
  on property: revised
subclass of: Restriction
  all values from: publication
  on property: supported_by
subclass of: Restriction
  all values from: boolean
  on property: is_inferred
subclass of: Restriction
  max cardinality: 1
  on property: release_date
subclass of: Restriction
  all values from: date
  on property: release_date
subclass of: Restriction
  min cardinality: 0
  on property: reviewed
subclass of: Restriction
  all values from: summation
  on property: has_summation
subclass of: Restriction
  all values from: disease
  on property: has_disease_context
subclass of: Restriction
  min cardinality: 0
  on property: has_disease_context
subclass of: Restriction
  min cardinality: 0
  on property: release_status
subclass of: Restriction
  min cardinality: 0
  on property: supported_by
subclass of: Restriction
  all values from: string
  on property: release_status
subclass of: Restriction
  min cardinality: 0
  on property: release_date
subclass of: Restriction
  max cardinality: 1
  on property: is_inferred
subclass of: Restriction
  all values from: database_identifier
  on property: has_cross_reference
subclass of: Restriction
  all values from: compartment
  on property: located_in_compartment
subclass of: Restriction
  min cardinality: 0
  on property: located_in_compartment
subclass of: Restriction
  min cardinality: 0
  on property: in_taxon
subclass of: database_object
definition: Biological occurrence or process unit in Reactome, covering both pathways and reaction-like events.
in scheme: reactome-ontology
note: Event is one of the central abstractions in the Reactome model.

reaction_like_event
type: Class
subclass of: Restriction
  all values from: physical_entity
  on property: has_input
subclass of: Restriction
  min cardinality: 0
  on property: has_catalyst_activity
subclass of: Restriction
  min cardinality: 0
  on property: preceded_by
subclass of: Restriction
  all values from: physical_entity
  on property: has_interacting_entity_on_other_cell
subclass of: Restriction
  min cardinality: 0
  on property: has_interaction
subclass of: Restriction
  min cardinality: 0
  on property: has_reaction_type
subclass of: Restriction
  all values from: catalyst_activity
  on property: has_catalyst_activity
subclass of: Restriction
  all values from: event
  on property: preceded_by
subclass of: Restriction
  min cardinality: 0
  on property: has_output
subclass of: Restriction
  min cardinality: 0
  on property: requires_component
subclass of: Restriction
  min cardinality: 0
  on property: has_regulation
subclass of: Restriction
  all values from: reaction_type_term
  on property: has_reaction_type
subclass of: Restriction
  all values from: physical_entity
  on property: requires_component
subclass of: Restriction
  all values from: regulation
  on property: has_regulation
subclass of: Restriction
  min cardinality: 0
  on property: has_input
subclass of: Restriction
  all values from: physical_entity
  on property: has_output
subclass of: Restriction
  min cardinality: 0
  on property: has_interacting_entity_on_other_cell
subclass of: Restriction
  all values from: interaction
  on property: has_interaction
subclass of: event
definition: Event in which physical entities participate as inputs, outputs, regulators, or catalysts in a transformation-like process.
in scheme: reactome-ontology
note: Covers canonical reactions as well as black-box and polymerization-style event subclasses.

instance_edit
type: Class
subclass of: Restriction
  min cardinality: 0
  on property: author
subclass of: Restriction
  all values from: dateTime
  on property: date
subclass of: Restriction
  min cardinality: 0
  on property: date
subclass of: Restriction
  all values from: person
  on property: author
subclass of: Restriction
  max cardinality: 1
  on property: date
subclass of: database_object
definition: Provenance record describing a curation action such as creation, modification, review, or revision.
in scheme: reactome-ontology
note: Typically stores who performed an edit and when the edit occurred.

database_object
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: source_schema_class
subclass of: Restriction
  all values from: string
  on property: definition
subclass of: Restriction
  max cardinality: 1
  on property: reactome_db_id
subclass of: Restriction
  max cardinality: 1
  on property: reactome_stable_identifier
subclass of: Restriction
  min cardinality: 0
  on property: previous_stable_identifier
subclass of: Restriction
  max cardinality: 1
  on property: previous_stable_identifier
subclass of: Restriction
  all values from: integer
  on property: reactome_db_id
subclass of: Restriction
  max cardinality: 1
  on property: created
subclass of: Restriction
  all values from: instance_edit
  on property: created
subclass of: Restriction
  all values from: string
  on property: reactome_stable_identifier
subclass of: Restriction
  min cardinality: 1
  on property: display_label
subclass of: Restriction
  min cardinality: 1
  on property: reactome_db_id
subclass of: Restriction
  min cardinality: 1
  on property: created
subclass of: Restriction
  max cardinality: 1
  on property: definition
subclass of: Restriction
  all values from: string
  on property: previous_stable_identifier
subclass of: Restriction
  all values from: instance_edit
  on property: modified
subclass of: Restriction
  all values from: string
  on property: display_label
subclass of: Restriction
  max cardinality: 1
  on property: display_label
subclass of: Restriction
  min cardinality: 1
  on property: reactome_stable_identifier
subclass of: Restriction
  min cardinality: 1
  on property: source_schema_class
subclass of: Restriction
  min cardinality: 0
  on property: definition
subclass of: Restriction
  all values from: string
  on property: source_schema_class
subclass of: Restriction
  min cardinality: 0
  on property: modified
subclass of: named_entity
definition: Root class for most Reactome schema objects and the main provenance-bearing superclass.
in scheme: reactome-ontology
note: Reactome’s frame-based model uses DatabaseObject as the common ancestor for curated graph records.

physical_entity
type: Class
subclass of: Restriction
  all values from: disease
  on property: has_disease_context
subclass of: Restriction
  all values from: database_identifier
  on property: has_cross_reference
subclass of: Restriction
  all values from: organism_taxon
  on property: in_taxon
subclass of: Restriction
  min cardinality: 0
  on property: is_in_disease_context
subclass of: Restriction
  max cardinality: 1
  on property: systematic_name
subclass of: Restriction
  max cardinality: 1
  on property: is_in_disease_context
subclass of: Restriction
  min cardinality: 0
  on property: has_disease_context
subclass of: Restriction
  min cardinality: 0
  on property: located_in_compartment
subclass of: Restriction
  all values from: boolean
  on property: is_in_disease_context
subclass of: Restriction
  min cardinality: 0
  on property: in_taxon
subclass of: Restriction
  max cardinality: 1
  on property: has_go_cellular_component
subclass of: Restriction
  all values from: go_cellular_component_term
  on property: has_go_cellular_component
subclass of: Restriction
  min cardinality: 0
  on property: systematic_name
subclass of: Restriction
  all values from: string
  on property: systematic_name
subclass of: Restriction
  min cardinality: 0
  on property: has_cross_reference
subclass of: Restriction
  all values from: compartment
  on property: located_in_compartment
subclass of: Restriction
  min cardinality: 0
  on property: has_go_cellular_component
subclass of: database_object
definition: Concrete biological participant whose identity reflects both underlying molecular identity and contextual state.
in scheme: reactome-ontology
note: In Reactome, compartment, modification state, and assembly state can distinguish one physical entity from another.