# Reactome MCP server

> Exposes the Reactome pathway knowledgebase to AI assistants for searching, browsing, and analyzing biological pathway data.

- Repository: https://github.com/reactome/reactome-mcp
- Page: https://hostedmcp.org/servers/reactome/reactome-mcp
- Transport: —
- Stars: 6
- License: Apache-2.0

## Environment variables

| Name | Required | Secret | Description |
|---|---|---|---|
| `MCP_ALLOW_CYPHER` | no | no |  |
| `MCP_HTTP_PORT` | no | no |  |
| `MCP_TOOL_GROUPS` | no | no |  |
| `NEO4J_DATABASE` | no | no |  |
| `NEO4J_PASSWORD` | no | no |  |
| `NEO4J_SCHEMA_FILE` | no | no |  |
| `NEO4J_URI` | no | no |  |
| `NEO4J_USER` | no | no |  |

## Tools (72)

- `search`
- `pathway`
- `entity`
- `analysis`
- `export`
- `interactors`
- `gsa`
- `utilities`
- `cypher`
- `unset`
- `reactome_analyze_identifier`
- `reactome_analyze_identifiers`
- `reactome_get_analysis_result`
- `reactome_analysis_found_entities`
- `reactome_analysis_not_found`
- `reactome_analysis_resources`
- `reactome_compare_species`
- `reactome_analysis_pathway_sizes`
- `reactome_filter_analysis_pathways`
- `reactome_get_pathway`
- `reactome_top_pathways`
- `reactome_pathway_ancestors`
- `reactome_pathway_contained_events`
- `reactome_pathways_for_entity`
- `reactome_diagram_pathways_for_entity`
- `reactome_events_hierarchy`
- `reactome_preceding_events`
- `reactome_search`
- `reactome_search_paginated`
- `reactome_search_suggest`
- `reactome_search_spellcheck`
- `reactome_search_facets`
- `reactome_search_pathways_of`
- `reactome_search_diagram`
- `reactome_get_entity`
- `reactome_complex_subunits`
- `reactome_entity_other_forms`
- `reactome_entity_component_of`
- `reactome_participants`
- `reactome_participating_physical_entities`
- `reactome_reference_entities`
- `reactome_complexes_containing`
- `reactome_export_diagram`
- `reactome_export_reaction`
- `reactome_export_fireworks`
- `reactome_export_sbgn`
- `reactome_export_sbml`
- `reactome_export_pdf`
- `reactome_export_analysis_report`
- `reactome_export_analysis_csv`
- `reactome_export_analysis_json`
- `reactome_psicquic_resources`
- `reactome_psicquic_summary`
- `reactome_psicquic_details`
- `reactome_static_interactors`
- `reactome_interactor_pathways`
- `reactome_interactor_summary`
- `reactome_gsa_methods`
- `reactome_gsa_data_types`
- `reactome_gsa_search_datasets`
- `reactome_gsa_examples`
- `reactome_gsa_sources`
- `reactome_species`
- `reactome_diseases`
- `reactome_database_info`
- `reactome_mapping_pathways`
- `reactome_mapping_reactions`
- `reactome_orthology`
- `reactome_query`
- `reactome_cypher_schema`
- `reactome_cypher_sample`
- `reactome_cypher_query`

## FAQ

### What can I do with the Reactome MCP server?

You can perform pathway enrichment analysis, search across pathways, proteins, and genes, browse pathway hierarchies, and export biological data in various formats.

### Can I query a graph database with this server?

Yes, internal instances can be granted read-only Cypher access to a Reactome Neo4j graph database by setting NEO4J_URI and MCP_ALLOW_CYPHER to 1.

### What formats can I export biological data in?

The server supports exporting diagrams in PNG, SVG, JPG, and GIF, as well as SBGN, SBML, PDF reports, and CSV/JSON analysis results.