reactome-mcp

An MCP (Model Context Protocol) server that exposes the Reactome pathway knowledgebase to AI assistants. It wraps Reactome's Content Service and Analysis Service REST APIs, giving LLMs the ability to search, browse, analyse, and export biological pathway data through natural language.

Features

• Pathway enrichment analysis — submit gene/protein lists and retrieve over-representation results, including p-values, FDR, and found/not-found identifiers
• Search — full-text search across pathways, reactions, proteins, genes, and compounds with faceting, pagination, autocomplete, and spellcheck
• Pathway browsing — navigate the pathway hierarchy, retrieve event details, ancestors, contained events, and participants
• Entity lookup — inspect physical entities, complexes, subunits, and cross-references
• Interactors — query protein–protein interaction data from PSICQUIC resources and Reactome's curated interactor database
• Export — diagrams (PNG/SVG/JPG/GIF), SBGN, SBML, PDF reports, and CSV/JSON analysis results
• Species & disease — list available species and disease annotations
• ID mapping — map external identifiers (UniProt, Ensembl, CHEBI, etc.) to Reactome pathways and reactions

Over 40 tools and 10 resources are registered — see Tools and Resources below for the full list.

Prerequisites

• Node.js >= 18

Installation

git clone https://github.com/reactome/reactome-mcp.git
cd reactome-mcp
npm install
npm run build

Usage

With Claude Desktop

Add the server to your Claude Desktop configuration (claude_desktop_config.json):

{
  "mcpServers": {
    "reactome": {
      "command": "node",
      "args": ["/absolute/path/to/reactome-mcp/dist/index.js"]
    }
  }
}

With Claude Code

claude mcp add reactome node /absolute/path/to/reactome-mcp/dist/index.js

Standalone

npm start

The server communicates over stdio using the MCP protocol.

MCP Inspector

npm run inspect

Opens the MCP Inspector UI for interactive testing.

Web Demo

npm run demo

Starts a local web UI with an MCP bridge for browser-based exploration.

Tools

Analysis (9 tools)

| Tool | Description | |------|-------------| | reactome_analyze_identifier | Analyse a single gene/protein identifier for pathway enrichment | | reactome_analyze_identifiers | Pathway enrichment analysis on a list of identifiers | | reactome_get_analysis_result | Retrieve a previously computed analysis result by token | | reactome_analysis_found_entities | Get identifiers found in a specific pathway from an analysis | | reactome_analysis_not_found | Get identifiers that could not be mapped in an analysis | | reactome_analysis_resources | Get a summary of molecule types found in an analysis | | reactome_compare_species | Compare Homo sapiens pathways to another species | | reactome_analysis_pathway_sizes | Get pathway size distribution from an analysis result | | reactome_filter_analysis_pathways | Filter an analysis result to specific pathways |

Pathways (7 tools)

| Tool | Description | |------|-------------| | reactome_get_pathway | Get details of a specific pathway or reaction | | reactome_top_pathways | List top-level pathways for a species | | reactome_pathway_ancestors | Get the ancestor hierarchy of an event | | reactome_pathway_contained_events | Get all events contained within a pathway | | reactome_pathways_for_entity | Find pathways containing a specific entity | | reactome_diagram_pathways_for_entity | Find diagram-level pathways containing an entity | | reactome_events_hierarchy | Get the complete event hierarchy for a species |

Search (7 tools)

| Tool | Description | |------|-------------| | reactome_search | Full-text search across the knowledgebase | | reactome_search_paginated | Search with pagination | | reactome_search_suggest | Autocomplete suggestions | | reactome_search_spellcheck | Spell-check suggestions | | reactome_search_facets | Get available search facets/filters | | reactome_search_pathways_of | Find pathways containing an entity by database ID | | reactome_search_diagram | Search for entities within a pathway diagram |

Entities (8 tools)

| Tool | Description | |------|-------------| | reactome_get_entity | Get details of a physical entity | | reactome_complex_subunits | Get all subunits of a complex | | reactome_entity_other_forms | Get other forms of a physical entity | | reactome_entity_component_of | Find larger structures containing an entity | | reactome_participants | Get molecular participants in a reaction or pathway | | reactome_participating_physical_entities | Get physical entities participating in an event | | reactome_reference_entities | Get reference entities for event participants | | reactome_complexes_containing | Find complexes containing an external identifier |

Export (9 tools)

| Tool | Description | |------|-------------| | reactome_export_diagram | Export a pathway diagram as an image | | reactome_export_reaction | Export a reaction diagram as an image | | reactome_export_fireworks | Export the species pathway overview diagram | | reactome_export_sbgn | Export to SBGN XML | | reactome_export_sbml | Export to SBML | | reactome_export_pdf | Export documentation to PDF | | reactome_export_analysis_report | Generate a PDF analysis report | | reactome_export_analysis_csv | Export analysis results as CSV | | reactome_export_analysis_json | Export analysis results as JSON |

Interactors (6 tools)

| Tool | Description | |------|-------------| | reactome_psicquic_resources | List available PSICQUIC interaction databases | | reactome_psicquic_summary | Summarise interactions from a PSICQUIC resource | | reactome_psicquic_details | Get detailed interactions from a PSICQUIC resource | | reactome_static_interactors | Get curated interactions from Reactome | | reactome_interactor_pathways | Find pathways where a protein's interactors appear | | reactome_interactor_summary | Summarise curated interactions for a protein |

Utilities (7 tools)

| Tool | Description | |------|-------------| | reactome_species | List species available in Reactome | | reactome_diseases | List diseases annotated in Reactome | | reactome_database_info | Get database version information | | reactome_mapping_pathways | Map an external identifier to pathways | | reactome_mapping_reactions | Map an external identifier to reactions | | reactome_orthology | Get orthologous events/entities in another species | | reactome_query | Query any Reactome database object by identifier |

Resources

Static

| URI | Description | |-----|-------------| | reactome://species | All species in Reactome | | reactome://species/main | Main species with curated pathways | | reactome://diseases | All annotated diseases | | reactome://database/info | Database version and name |

Templates

| URI Template | Description | |--------------|-------------| | reactome://pathway/{id} | Pathway details | | reactome://pathway/{id}/diagram | Pathway diagram (SVG) | | reactome://entity/{id} | Entity details | | reactome://analysis/{token} | Analysis result | | reactome://top-pathways/{species} | Top-level pathways for a species | | reactome://events-hierarchy/{species} | Full event hierarchy for a species |

Development

npm run dev       # watch mode — recompiles on changes
npm run inspect   # interactive MCP Inspector
npm run demo      # web demo with MCP bridge

License

This project is licensed under the Apache License 2.0 — see LICENSE for details.