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.
Administrative and serialization helper fields are retained for round-tripping but may be omitted from OWL export profiles.
Inverse-style helper relations have been removed from the ontology-facing profile in favor of canonical relations.
This schema favors ontology-oriented naming for OWL generation; source mappings are maintained in separate mapping files.
Top-level container for a serialized Reactome dataset excerpt or export package.
Provides a practical root object for JSON and YAML instance data.
Provenance links capturing authoring actions for the object.
Included to support richer editorial provenance when present in exports.
Explicit category designator used in serialized instances.
Useful when data are exchanged in JSON or YAML and class typing must be preserved.
Reaction-like event included in the pathway model despite incomplete mechanistic detail.
Useful when biological evidence supports the event but not a full molecular mechanism.
Entity set whose members are candidates for fulfilling a shared biological role.
Often reflects partial knowledge or broad functional grouping.
Cell or cell-like biological unit treated as a physical participant in an event.
Included for cases where cells themselves are modeled as interacting biological entities.
Drug represented primarily as a chemical or small-molecule therapeutic agent.
Often alignable to small-molecule reference identities.
Physical entity composed of two or more component physical entities assembled into a functional complex.
The complex is treated as an entity distinct from its components.
Entity set whose members are explicitly curated as the intended interchangeable participants.
Stronger editorial commitment than a candidate set.
Event representing breakdown of a polymer into constituent or smaller units.
Literature citation record, commonly representing a PubMed-indexed paper supporting a Reactome assertion.
Used widely to ground events, regulations, and catalyst activities in the literature.
Regulation that decreases, inhibits, or negatively influences the occurrence or efficiency of a reaction-like event.
Semantic polarity is explicit at the class level.
Catch-all physical entity class for biologically relevant participants not covered by more specific subclasses.
Helps preserve source fidelity when Reactome uses residual categorization.
Curated grouping of biologically related events representing a pathway or pathway-like module.
Pathways can overlap; event membership is not exclusive.
Polymer entity abstracted in terms of one or more repeated units.
Useful for biological polymers that are not modeled by enumerating every monomer instance.
Event representing formation of a polymer from repeated or assembling units.
Kept distinct because its participant semantics can differ from ordinary reaction balance.
Regulation that increases, enables, or positively influences the occurrence or efficiency of a reaction-like event.
Drug represented as a protein therapeutic or protein-derived biologic.
Includes antibody-like or recombinant protein therapeutics when modeled as physical entities.
Standard reaction-like event with explicit transformed inputs and outputs.
Best used for relatively well-resolved mechanistic conversions.
Supports DNA-centric entities in the Reactome schema.
Reference sequence corresponding to a gene product, typically protein-centric.
Often alignable to UniProt entries for proteins.
Grouped reference identity used when an invariant identity is represented at a grouped rather than single-entry level.
Useful for families or grouped reference semantics in source data.
Reference sequence representing a specific isoform-level identity.
Useful when isoform distinction matters biologically.
Supports transcript and RNA molecule identity modeling.
Reference identity for a therapeutic or intervention-oriented entity.
Supports the reference-layer counterpart of drug-like modeled entities.
Regulation-like assertion indicating that a regulator or participant is required for a reaction-like event to occur.
Used when necessity is the key biological relation rather than positive or negative modulation.
Drug represented as an RNA-based therapeutic agent.
Can cover antisense, siRNA, or related RNA therapeutic modalities.
Sequence-bearing physical entity linked to a stable reference sequence and optionally decorated with residue modifications and subsequence coordinates.
Core Reactome pattern for proteins, RNAs, and other accessioned biomolecules in specific states.
Simple molecular entity, typically a small molecule or other non-sequence-based chemical participant.
Commonly aligned to ChEBI-like reference identities through ReferenceMolecule.
Taxonomic concept used for taxonomic assignment or metadata.
Can be used in parallel with or beneath species-oriented records.
Physical entity whose existence is grounded in a genome-encoded product such as a protein or nucleic acid.
Serves as a superclass for accessioned sequence-based entities.
Generic named entity used as a lightweight semantic root for serializable objects.
Provides reusable identifier, naming, and descriptive slots independent of the Reactome-specific hierarchy.
Person record used primarily for provenance, authorship, and curation attribution.
May represent curators, reviewers, or contributors.
Reference identity for a small molecule, simple chemical, or chemically grounded participant.
Naturally alignable to ChEBI-like references.
Person or people responsible for the edit activity.
Reaction-like event catalyzed by the given catalyst activity.
Allows one catalyst activity node to connect molecular function and event participation.
Collection of Reactome objects keyed by identifier.
Catalyst activity associated with the reaction-like event.
A central Reactome modeling pattern that preserves GO molecular function and active-unit context.
Component physical entities that make up a complex.
Complex identity is distinct from component identity in Reactome.
Membership relation linking a pathway to constituent events.
Pathways in Reactome are curated groupings of events and can overlap with other pathways.
Physical entity located on another interacting cell in intercellular biology.
Useful for immune, adhesion, and receptor-ligand interaction contexts.
Associated interaction object linked to an event.
Preserves interaction-level detail when Reactome models such assertions explicitly.
Members of an entity set representing functionally interchangeable participants.
Entity sets are curated graph objects, not simply OWL classes over their members.
Modified residue feature borne by a sequence-based physical entity.
Supports phosphorylation, cleavage, ubiquitination, and related residue-level state modeling.
Controlled reaction type annotation describing the mechanistic or editorial type of a reaction.
Useful for grouping reaction-like events into broad mechanistic categories.
Reified regulation assertion attached to an event.
Supports positive, negative, and requirement-style regulatory semantics.
Repeated unit composing a polymer entity.
Used when Reactome models a polymer abstractly in terms of repeating constituents.
Provenance links to subsequent modifications of the object record.
Multiple modifications are common across curation history.
Event that occurs before the current event in a curated process sequence.
Encodes partial ordering rather than necessarily strict temporal or causal completeness.
Physical entity required for a reaction-like event but not modeled as a transforming input.
Useful for contextual cofactors, platform components, or required participants.
Provenance links to formal review actions on the object.
Distinct from simple modification in Reactome curation workflows.
Provenance links to explicit revision actions after prior curation or review.
Useful for tracking editorial iteration.
Feature record describing a modified residue or residue-level state on a sequence-bearing entity.
Abstract superclass for phosphorylation-like or other residue modification records.
Reified catalytic assertion connecting a catalyst bearer, a GO molecular function, and one or more catalyzed reaction-like events.
This is one of the most semantically important reified node types in Reactome.
Curated set of physical entities that are treated as functionally interchangeable in a given biological context.
This is a graph object representing a curated set, not merely a class extension over its members.
Wrapper object for a GO biological process term used for pathway or event alignment.
Useful for crosswalks between Reactome pathways and GO process knowledge.
Wrapper object for a GO cellular component term used in entity or location annotation.
Often complements explicit compartment modeling.
Wrapper object for a GO molecular function term used in Reactome catalysis modeling.
Particularly important in CatalystActivity.
Interaction record associated with an event or set of participants.
Retained as a distinct object to preserve graph fidelity when interactions are explicitly modeled.
Controlled vocabulary term used to characterize a reaction-like event.
Supports editorial or mechanistic grouping of reaction events.
Narrative summary record containing prose that explains the biological meaning of an entity or event.
Distinct from a formal definition; meant for human reading.
URL template or access URL used to resolve an identifier in a reference database.
Can encode direct or templated resolver behavior.
Provenance link to the curation event that originally created the object record.
Usually points to an InstanceEdit containing editor and date metadata.
Timestamp or date string for the edit activity.
Curated textual definition that states what the object is.
Intended for conceptual definitions rather than narrative summaries.
Free-text textual description of an object.
Can hold editorial notes, plain-language explanations, or short summaries.
Preferred display label used by Reactome for user-facing presentation.
Often combines identity and contextual state into a concise label.
End coordinate of a subsequence, fragment, or feature-bearing region on a sequence entity.
Physical entity serving as the bearer of a catalyst activity.
Used inside reified catalyst activity objects.
GO biological process term associated with a Reactome pathway or event.
Useful as a high-level semantic alignment rather than an exact equivalence in all cases.
GO cellular component term associated with a physical entity or event context.
Often complements the explicit compartment modeling in Reactome.
GO molecular function term asserted in a catalyst activity.
Reactome reifies catalysis so the molecular function can be attached explicitly.
Physical entity that exerts regulatory influence on a regulated event.
May be a protein, complex, small molecule, set, or other physical entity.
Narrative summary object explaining the biology of an event or entity.
Distinct from formal definition; usually prose intended for readers.
Unique identifier for an instance in the serialized dataset.
This may be a local identifier, CURIE, URI, or other serialization key.
Prefix or namespace abbreviation used by a reference database.
Useful for CURIE generation and namespace harmonization.
Boolean flag indicating that the represented entity is contextualized to a disease state.
This is a contextual flag and does not by itself define a disease ontology class.
Indicates whether an object was computationally inferred rather than directly curated.
Reactome uses inference especially for orthology-based event propagation.
ORCID identifier for a person involved in curation or authorship.
Useful for curator and contributor disambiguation.
Deprecated or previous stable Reactome identifier retained for traceability.
Useful during migration, identifier replacement, and legacy resolution.
PubMed identifier for a literature reference.
Stored as string for broad interoperability with exports and loaders.
Internal Reactome database identifier assigned to a database object.
Reactome DB_ID values are implementation-oriented identifiers rather than stable public identifiers.
Stable public Reactome identifier for an object.
Typically corresponds to the curated Reactome stable accession such as R-HSA-xxxxx.
Reaction-like event that is the target of regulation.
Kept explicit through reified regulation nodes rather than flattened triples.
Release date associated with a curation or publication cycle.
Modeled as string to match Reactome exports; can be normalized later if needed.
Editorial release state of the object in the Reactome release process.
Examples might include draft-like or released-like status labels depending on source exports.
Identifier for the reference resource itself rather than for entries inside it.
Supports metadata about the authority record for a database.
Textual qualifier for the kind of referenced sequence or entity.
Included for compatibility with Reactome exports.
Name of the source Reactome schema class from which the instance derives.
Useful when preserving frame-schema provenance or round-tripping with the original Reactome graph.
Start coordinate of a subsequence, fragment, or feature-bearing region on a sequence entity.
Useful for proteolytic fragments, domains, and sequence-trimmed entity forms.
Formal or systematic name for an entity when available.
Often useful for chemicals, complexes, or sequence-derived entities.
Often used for resource metadata pages or resolver entry points.
Cellular or subcellular location object used to state where an event occurs or where a physical entity resides.
Often alignable to GO cellular component terms, though not always identical in role.
Cross-reference record that pairs an identifier string with a reference database authority.
Useful as a reified identifier object rather than a bare literal.
Disease concept used to contextualize events and entities in pathological settings.
Represents disease context rather than a full disease ontology commitment.
Therapeutic or intervention-oriented physical entity modeled in the Reactome graph.
Drug subclasses distinguish broad molecular kinds of therapeutic agents.
Organism taxon record representing the organismal context for entities and events.
Often associated with taxonomy identifiers and may correspond to NCBI Taxonomy concepts.
Metadata record describing an external database or authority used for identifiers and cross-references.
Holds resolver and namespace information for identifier interpretation.
Subunit, domain-bearing fragment, or active molecular portion responsible for catalytic or regulatory activity.
Reactome can attach active-unit detail to catalyst activities and regulation objects.
External cross-reference to another database or controlled resource.
Used for interoperating with identifiers from GO, ChEBI, UniProt, Ensembl, and related resources.
Disease context associated with an event or physical entity.
Represents contextual disease association rather than broad etiologic modeling.
Physical entity consumed, transformed, or otherwise used as an input to a reaction-like event.
Inputs need not always be fully consumed in a strict stoichiometric sense across all event subclasses.
Physical entity produced by a reaction-like event.
Output identity often reflects new compartment, modification state, or assembly state.
Taxon in which the object, event, or entity is asserted to occur or be defined.
For events this denotes the organism context; for entities it denotes the biological source organism.
Compartment in which an entity resides or an event occurs.
In Reactome, compartment is identity-relevant for many physical entities.
Human-readable primary label for an object.
Generic reusable naming slot for schema-wide use.
Publication record used as evidence or supporting documentation for curated biology.
Abstract superclass for specific publication-like records.
Invariant reference identity used to connect multiple contextualized physical entities that share an underlying molecular identity.
This is the key abstraction Reactome uses to separate contextual state from canonical identity.
Reference identity for a sequence-bearing biomolecule.
Commonly used for protein, DNA, RNA, and isoform references.
Reified regulatory assertion linking a regulator physical entity to a regulated reaction-like event.
Reactome models regulation explicitly instead of flattening it into a simple binary relation.
Reference database authority associated with a reference entity or database identifier.
Provides the namespace and interpretation context for an identifier.
Invariant reference identity underlying a contextualized physical entity.
{'One of the key distinctions in Reactome': 'reference identity is separate from stateful physical instantiation.'}
Identifier string assigned by an external reference database.
Examples include UniProt accessions, ChEBI identifiers, or GO term identifiers.
Taxonomic identifier, typically aligned to the NCBI Taxonomy.
Often used on species or taxon-like records.
Publication supporting the existence, mechanism, or curation of the object.
Often points to PubMed-backed literature references.
Biological occurrence or process unit in Reactome, covering both pathways and reaction-like events.
Event is one of the central abstractions in the Reactome model.
Event in which physical entities participate as inputs, outputs, regulators, or catalysts in a transformation-like process.
Covers canonical reactions as well as black-box and polymerization-style event subclasses.
Provenance record describing a curation action such as creation, modification, review, or revision.
Typically stores who performed an edit and when the edit occurred.
Root class for most Reactome schema objects and the main provenance-bearing superclass.
Reactome’s frame-based model uses DatabaseObject as the common ancestor for curated graph records.
Concrete biological participant whose identity reflects both underlying molecular identity and contextual state.
In Reactome, compartment, modification state, and assembly state can distinguish one physical entity from another.