Which integrations are available for this server?

Provides Cypher query access to a local Reactome Neo4j graph database, enabling curation and graph-based exploration of pathway data.

How do I use reactome-mcp?

1. Click on "Install Server". 2. Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state. 3. In the chat, type @ followed by the MCP server name and your instructions, e.g., "@reactome-mcp Find pathways involving the TP53 gene" That's it! The server will respond to your query, and you can continue using it as needed. Here is a step-by-step guide with screenshots.

reactome-mcp

Official

by reactome

Overview Schema Related Servers Score Discussions

TypeScript

Remote

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. Curators can additionally opt in to direct Cypher / Neo4j access against a local Reactome graph database (see Graph Database / Cypher).

Related MCP server: KEGG MCP Server

Prerequisites

Node.js >= 18

Installation

git clone https://github.com/reactome/reactome-mcp.git
cd reactome-mcp
npm install  # runs `prepare` which builds dist/

Configuration

All configuration is via environment variables — pass them in the env block of your MCP client config.

Variable	Default	Purpose
`REACTOME_BASE_URL`	`https://reactome.org`	Base URL for the Content + Analysis Services. Override to point at staging / a specific release host.
`REACTOME_CONTENT_SERVICE_URL`	derived from `REACTOME_BASE_URL`	Fine-grained override for the Content Service only.
`REACTOME_ANALYSIS_SERVICE_URL`	derived from `REACTOME_BASE_URL`	Fine-grained override for the Analysis Service only.
`NEO4J_URI`	(unset)	Set to enable the optional Cypher tools (see below).
`NEO4J_USER`	`neo4j`
`NEO4J_PASSWORD`	`neo4j`	Works against auth-disabled local images (`reactome_neo4j_env`). Set explicitly for any remote database.
`NEO4J_DATABASE`	`graph.db`	Matches the default in `reactome_neo4j_env`.
`CYPHER_QUERY_TIMEOUT_MS`	`30000`	Server-side transaction timeout (ms) for `reactome_cypher_*` tools. Runaway queries are terminated after this.
`LOG_LEVEL`	`info`	`debug` / `info` / `warn` / `error`. Logs are JSON on stderr; stdout is reserved for the MCP protocol.

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

Add --env NEO4J_URI=bolt://localhost:7687 (and friends) to enable the Cypher tools. See Configuration for the full list.

Example prompts

Once the server is registered, try asking Claude:

Exploration (REST — works with default install):

"What does Reactome know about the TP53 gene? Show me the top pathways it appears in."
"Give me the top-level pathways for Mus musculus and point out which are disease pathways."
"Summarize pathway R-HSA-109582 — include the references."
"I have these UniProt IDs: P04637, P53350, Q9UPN9, Q9Y243. Run a Reactome pathway enrichment and list the top 10 hits by FDR."
"Find pathways in the HHV8 infection area and show me the contained reactions of the best match."
"Export the SBGN for pathway R-HSA-1640170."

Graph queries (requires NEO4J_URI):

"Show me the Reactome graph schema, then find all Pathway nodes that are disease pathways and have a human species annotation."
"Using the graph DB: for reaction R-HSA-199420, list every input and output entity with its display name and stable ID."
"Count how many ReactionLikeEvent nodes exist per species."

Claude reads per-server instructions on connection explaining the tool categories, ID conventions, and a recommended workflow, so it can usually chain the right calls without hand-holding. If an answer looks off, ask it to "show me the tool call and its result" and correct from there.

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

Graph Database / Cypher (3 tools, opt-in)

Only registered when NEO4J_URI is set. Designed for curators running the reactome_neo4j_env Docker image locally (or pointing at a remote Reactome Neo4j).

Tool	Description
`reactome_cypher_query`	Run a Cypher query with optional parameters; row count, per-row size, and total response size are all capped; a server-side timeout terminates runaway queries
`reactome_cypher_schema`	Live APOC introspection: labels with node counts, relationship cardinalities, per-label and per-rel property types (with mandatory flags), indexes, constraints. Cached for the session after first call; pre-warmed at MCP startup.
`reactome_cypher_sample`	Return a small sample of nodes for a given label

Read-only posture — what it is and isn't. Sessions run in Neo4j READ mode, which rejects native write clauses (CREATE, MERGE, DELETE, SET, REMOVE). On top of that, reactome_cypher_query rejects APOC procedures that can write or reach outside the graph through back-channels (apoc.cypher.runWrite / apoc.cypher.doIt, apoc.periodic.*, apoc.create/merge/refactor.*, apoc.load/import/export.*, apoc.trigger.*, apoc.nodes.delete). Treat this as a guardrail against accidental mutation, not a security boundary — a real trust boundary should live at the Neo4j RBAC / plugin configuration layer, or by pointing at a read-only replica.

Configuration (add to your Claude MCP config env block):

{
  "mcpServers": {
    "reactome": {
      "command": "node",
      "args": ["/absolute/path/to/reactome-mcp/dist/index.js"],
      "env": {
        "NEO4J_URI": "bolt://localhost:7687",
        "NEO4J_USER": "neo4j",
        "NEO4J_PASSWORD": "neo4j",
        "NEO4J_DATABASE": "graph.db",
        "CYPHER_QUERY_TIMEOUT_MS": "30000"
      }
    }
  }
}

NEO4J_USER / NEO4J_PASSWORD default to neo4j / neo4j (which works when the server has auth disabled, as in reactome_neo4j_env). NEO4J_DATABASE defaults to graph.db. CYPHER_QUERY_TIMEOUT_MS defaults to 30000 ms.

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.

This server cannot be installed

license - permissive license

quality - not tested

maintenance

How are these scores calculated?

Maintenance

–Maintainers

–Response time

–Release cycle

–Releases (12mo)

Commit activity

Resources

GitHub Repository

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