Reactome Ontology Model
The Reactome Ontology Model provides a more ontology-oriented and reusable representation of core parts of the Reactome data model. Using LinkML as the source schema, it describes entities, events, provenance, and related reference objects in a consistent and structured way. The model covers pathways, reactions, physical entities, regulatory relationships, and supporting metadata through clearly defined classes, slots, and ranges. This supports validation, documentation generation, ontology export, and downstream integration. Its goal is to provide a clear and interoperable foundation for publishing and working with Reactome knowledge in ontology-friendly formats.
URI: https://w3id.org/reactome-ontology
Name: reactome_ontology
Classes
| Class | Description |
|---|---|
| NamedEntity | Generic named entity used as a lightweight semantic root for serializable obj... |
| DatabaseObject | Root class for most Reactome schema objects and the main provenance-bearing s... |
| AbstractModifiedResidue | Feature record describing a modified residue or residue-level state on a sequ... |
| CatalystActivity | Reified catalytic assertion connecting a catalyst bearer, a GO molecular func... |
| Compartment | Cellular or subcellular location object used to state where an event occurs o... |
| DatabaseIdentifier | Cross-reference record that pairs an identifier string with a reference datab... |
| Disease | Disease concept used to contextualize events and entities in pathological set... |
| Event | Biological occurrence or process unit in Reactome, covering both pathways and... |
| Pathway | Curated grouping of biologically related events representing a pathway or pat... |
| ReactionLikeEvent | Event in which physical entities participate as inputs, outputs, regulators, ... |
| BlackBoxEvent | Reaction-like event included in the pathway model despite incomplete mechanis... |
| Depolymerization | Event representing breakdown of a polymer into constituent or smaller units |
| Polymerization | Event representing formation of a polymer from repeated or assembling units |
| Reaction | Standard reaction-like event with explicit transformed inputs and outputs |
| GoBiologicalProcessTerm | Wrapper object for a GO biological process term used for pathway or event ali... |
| GoCellularComponentTerm | Wrapper object for a GO cellular component term used in entity or location an... |
| GoMolecularFunctionTerm | Wrapper object for a GO molecular function term used in Reactome catalysis mo... |
| InstanceEdit | Provenance record describing a curation action such as creation, modification... |
| Interaction | Interaction record associated with an event or set of participants |
| OrganismTaxon | Organism taxon record representing the organismal context for entities and ev... |
| Person | Person record used primarily for provenance, authorship, and curation attribu... |
| PhysicalEntity | Concrete biological participant whose identity reflects both underlying molec... |
| Cell | Cell or cell-like biological unit treated as a physical participant in an eve... |
| Complex | Physical entity composed of two or more component physical entities assembled... |
| Drug | Therapeutic or intervention-oriented physical entity modeled in the Reactome ... |
| ChemicalDrug | Drug represented primarily as a chemical or small-molecule therapeutic agent |
| ProteinDrug | Drug represented as a protein therapeutic or protein-derived biologic |
| RnaDrug | Drug represented as an RNA-based therapeutic agent |
| EntitySet | Curated set of physical entities that are treated as functionally interchange... |
| CandidateSet | Entity set whose members are candidates for fulfilling a shared biological ro... |
| DefinedSet | Entity set whose members are explicitly curated as the intended interchangeab... |
| GenomeEncodedEntity | Physical entity whose existence is grounded in a genome-encoded product such ... |
| SequenceEntity | Sequence-bearing physical entity linked to a stable reference sequence and op... |
| Protein | Protein physical entity linked to a reference gene product and optionally dec... |
| OtherEntity | Catch-all physical entity class for biologically relevant participants not co... |
| Polymer | Polymer entity abstracted in terms of one or more repeated units |
| SimpleEntity | Simple molecular entity, typically a small molecule or other non-sequence-bas... |
| Publication | Publication record used as evidence or supporting documentation for curated b... |
| LiteratureReference | Literature citation record, commonly representing a PubMed-indexed paper supp... |
| ReactionTypeTerm | Controlled vocabulary term used to characterize a reaction-like event |
| ReferenceDatabase | Metadata record describing an external database or authority used for identif... |
| ReferenceEntity | Invariant reference identity used to connect multiple contextualized physical... |
| ReferenceGroup | Grouped reference identity used when an invariant identity is represented at ... |
| ReferenceMolecule | Reference identity for a small molecule, simple chemical, or chemically groun... |
| ReferenceSequence | Reference identity for a sequence-bearing biomolecule |
| ReferenceDnaSequence | Reference identity for a DNA sequence |
| ReferenceGeneProduct | Reference sequence corresponding to a gene product, typically protein-centric |
| ReferenceIsoform | Reference sequence representing a specific isoform-level identity |
| ReferenceRnaSequence | Reference identity for an RNA sequence |
| ReferenceTherapeutic | Reference identity for a therapeutic or intervention-oriented entity |
| Regulation | Reified regulatory assertion linking a regulator physical entity to a regulat... |
| NegativeRegulation | Regulation that decreases, inhibits, or negatively influences the occurrence ... |
| PositiveRegulation | Regulation that increases, enables, or positively influences the occurrence o... |
| Requirement | Regulation-like assertion indicating that a regulator or participant is requi... |
| Summation | Narrative summary record containing prose that explains the biological meanin... |
| Taxon | Taxonomic concept used for taxonomic assignment or metadata |
| ReactomeDataset | Top-level container for a serialized Reactome dataset excerpt or export packa... |
Slots
| Slot | Description |
|---|---|
| access_url | URL template or access URL used to resolve an identifier in a reference datab... |
| author | Person or people responsible for the edit activity |
| authored | Provenance links capturing authoring actions for the object |
| catalyzes | Reaction-like event catalyzed by the given catalyst activity |
| category | Explicit category designator used in serialized instances |
| created | Provenance link to the curation event that originally created the object reco... |
| database_objects | Collection of Reactome objects keyed by identifier |
| date | Timestamp or date string for the edit activity |
| definition | Curated textual definition that states what the object is |
| description | Free-text textual description of an object |
| display_label | Preferred display label used by Reactome for user-facing presentation |
| end_coordinate | End coordinate of a subsequence, fragment, or feature-bearing region on a seq... |
| has_active_unit | Subunit, domain-bearing fragment, or active molecular portion responsible for... |
| has_catalyst | Physical entity serving as the bearer of a catalyst activity |
| has_catalyst_activity | Catalyst activity associated with the reaction-like event |
| has_component | Component physical entities that make up a complex |
| has_cross_reference | External cross-reference to another database or controlled resource |
| has_disease_context | Disease context associated with an event or physical entity |
| has_event | Membership relation linking a pathway to constituent events |
| has_go_biological_process | GO biological process term associated with a Reactome pathway or event |
| has_go_cellular_component | GO cellular component term associated with a physical entity or event context |
| has_go_molecular_function | GO molecular function term asserted in a catalyst activity |
| has_input | Physical entity consumed, transformed, or otherwise used as an input to a rea... |
| has_interacting_entity_on_other_cell | Physical entity located on another interacting cell in intercellular biology |
| has_interaction | Associated interaction object linked to an event |
| has_member | Members of an entity set representing functionally interchangeable participan... |
| has_modified_residue | Modified residue feature borne by a sequence-based physical entity |
| has_output | Physical entity produced by a reaction-like event |
| has_reaction_type | Controlled reaction type annotation describing the mechanistic or editorial t... |
| has_reference_database | Reference database authority associated with a reference entity or database i... |
| has_reference_entity | Invariant reference identity underlying a contextualized physical entity |
| has_regulation | Reified regulation assertion attached to an event |
| has_regulator | Physical entity that exerts regulatory influence on a regulated event |
| has_repeated_unit | Repeated unit composing a polymer entity |
| has_summation | Narrative summary object explaining the biology of an event or entity |
| id | Unique identifier for an instance in the serialized dataset |
| identifier | Identifier string assigned by an external reference database |
| identifier_prefix | Prefix or namespace abbreviation used by a reference database |
| in_taxon | Taxon in which the object, event, or entity is asserted to occur or be define... |
| is_in_disease_context | Boolean flag indicating that the represented entity is contextualized to a di... |
| is_inferred | Indicates whether an object was computationally inferred rather than directly... |
| located_in_compartment | Compartment in which an entity resides or an event occurs |
| modified | Provenance links to subsequent modifications of the object record |
| name | Human-readable primary label for an object |
| ncbi_taxon_id | Taxonomic identifier, typically aligned to the NCBI Taxonomy |
| orcid | ORCID identifier for a person involved in curation or authorship |
| preceded_by | Event that occurs before the current event in a curated process sequence |
| previous_stable_identifier | Deprecated or previous stable Reactome identifier retained for traceability |
| pubmed_id | PubMed identifier for a literature reference |
| reactome_db_id | Internal Reactome database identifier assigned to a database object |
| reactome_stable_identifier | Stable public Reactome identifier for an object |
| regulates | Reaction-like event that is the target of regulation |
| release_date | Release date associated with a curation or publication cycle |
| release_status | Editorial release state of the object in the Reactome release process |
| requires_component | Physical entity required for a reaction-like event but not modeled as a trans... |
| resource_identifier | Identifier for the reference resource itself rather than for entries inside i... |
| reviewed | Provenance links to formal review actions on the object |
| revised | Provenance links to explicit revision actions after prior curation or review |
| sequence_reference_type | Textual qualifier for the kind of referenced sequence or entity |
| source_schema_class | Name of the source Reactome schema class from which the instance derives |
| start_coordinate | Start coordinate of a subsequence, fragment, or feature-bearing region on a s... |
| supported_by | Publication supporting the existence, mechanism, or curation of the object |
| systematic_name | Formal or systematic name for an entity when available |
| text | Narrative summary text |
| url | General URL associated with an object |
Enumerations
| Enumeration | Description |
|---|---|
Types
| Type | Description |
|---|---|
| Boolean | A binary (true or false) value |
| Curie | a compact URI |
| Date | a date (year, month and day) in an idealized calendar |
| DateOrDatetime | Either a date or a datetime |
| Datetime | The combination of a date and time |
| Decimal | A real number with arbitrary precision that conforms to the xsd:decimal speci... |
| Double | A real number that conforms to the xsd:double specification |
| Float | A real number that conforms to the xsd:float specification |
| Integer | An integer |
| Jsonpath | A string encoding a JSON Path |
| Jsonpointer | A string encoding a JSON Pointer |
| Ncname | Prefix part of CURIE |
| Nodeidentifier | A URI, CURIE or BNODE that represents a node in a model |
| Objectidentifier | A URI or CURIE that represents an object in the model |
| Sparqlpath | A string encoding a SPARQL Property Path |
| String | A character string |
| Time | A time object represents a (local) time of day, independent of any particular... |
| Uri | a complete URI |
| Uriorcurie | a URI or a CURIE |
Subsets
| Subset | Description |
|---|---|