Analyze a single gene/protein identifier for pathway enrichment. Returns pathways containing this identifier.

Perform pathway enrichment analysis on a list of gene/protein identifiers. Returns over-represented pathways sorted by p-value.

Retrieve a previously computed analysis result using its token. Allows filtering and pagination.

Get the identifiers that were found in a specific pathway from an analysis result.

Get the list of identifiers that could not be mapped in an analysis.

Get a summary of the molecule types (resources) found in an analysis.

Compare Homo sapiens pathways to another species to identify orthologous pathways.

Get the distribution of pathway sizes (binned) from an analysis result.

Filter an analysis result to only include specific pathways.

Get detailed information about a specific pathway or reaction by its Reactome ID.

Get all top-level (root) pathways for a species. These are the main pathway categories like 'Immune System', 'Metabolism', etc.

Get the ancestor pathway hierarchy for an event (pathway or reaction). Shows how a pathway fits into the broader Reactome structure.

Get all events (sub-pathways and reactions) contained within a pathway.

Find lower-level pathways that contain a specific entity (protein, gene, compound, etc.).

Find pathways with diagrams that contain a specific entity. Useful for visualization.

Get the complete event hierarchy (pathways and reactions tree) for a species. Warning: This returns a large data structure.

Search the Reactome knowledgebase for pathways, reactions, proteins, genes, compounds, and other entities.

Search Reactome with pagination support for browsing through large result sets.

Get auto-complete suggestions for a search query.

Get spell-check suggestions for a search query.

Get available facets (filters) for search results, either globally or for a specific query.

Find all pathways that contain a specific entity by its database ID.

Search for entities within a specific pathway diagram.

Get detailed information about a physical entity (protein, complex, compound, etc.) by its Reactome ID.

Get all subunits (components) of a complex. Recursively retrieves components of nested complexes.

Get all other forms of a physical entity (modified forms, in different compartments, in complexes, etc.).

Find larger structures (complexes, sets) that contain this entity as a component.

Get all molecular participants (inputs, outputs, catalysts, regulators) in a reaction or pathway.

Get all physical entities participating in an event (molecules directly involved in reactions).

Get all reference entities (external database references) for participants in an event.

Find all Reactome complexes that contain a specific external identifier (e.g., UniProt ID).

Export a pathway diagram as an image. Returns the URL to download the diagram.

Export a reaction diagram as an image.

Export the pathway overview (fireworks) diagram for a species.

Export a pathway or reaction to SBGN (Systems Biology Graphical Notation) XML format.

Export a pathway or reaction to SBML (Systems Biology Markup Language) format.

Export pathway or reaction documentation to PDF format.

Generate a PDF report for an analysis result.

Export analysis results as CSV files.

Export complete analysis result as JSON.

List available PSICQUIC registry services for protein-protein interaction data.

Get a summary of protein-protein interactions from a PSICQUIC resource.

Get detailed protein-protein interactions from a PSICQUIC resource.

Get curated protein-protein interactions from Reactome's static interactor database.

Find Reactome pathways where the interactors of a protein are found.

Get a summary of curated interactions for a protein.

Run a Cypher query against the local Reactome Neo4j graph database. The session runs in READ mode, which rejects native write clauses (CREATE/MERGE/DELETE/SET/REMOVE). APOC procedures that can write through that guardrail (apoc.cypher.runWrite, apoc.periodic., apoc.create/merge/refactor., apoc.load/import/export., apoc.trigger., apoc.nodes.delete) are rejected before execution. Row count, per-row size, and total response size are capped; a query timeout terminates runaway queries. Use LIMIT and project specific fields in your query for large results.

Introspect the Reactome graph schema — labels with node counts, relationship types with cardinalities, per-label and per-rel property types (with mandatory flags), indexes, and constraints. Fetched live from the database via APOC on first call and cached in-memory for the rest of the session (~100–300 ms one-time). Call this before writing Cypher. For the full JSON (including the raw apoc.meta.schema() object), read the reactome://graph/schema resource.

Return a small sample of nodes for a given label, to inspect shape and typical property values.

Get the list of species available in Reactome.

Get the list of diseases annotated in Reactome.

Get Reactome database version and name information.

Map an external identifier to Reactome pathways.

Map an external identifier to Reactome reactions.

Get orthologous events or entities in a different species.

Query any Reactome database object by its identifier. Returns detailed information about the object.