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Reactome MCP Server

by Augmented-Nature
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MIT License
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Unofficial Reactome MCP Server 🧬

Model Context Protocol server for accessing Reactome pathway and systems biology data.

API

Developed by Augmented Nature - Advancing AI for Scientific Discovery

✅ Verified Features

All 8 tools working with live Reactome API data:

  • 🔍 Pathway Search - Search biological pathways by name, process, keywords

  • 📊 Pathway Details - Comprehensive pathway information and components

  • 🧬 Gene-to-Pathways - Find pathways containing specific genes/proteins

  • 🦠 Disease Pathways - Disease-associated biological mechanisms

  • 🌲 Pathway Hierarchy - Parent/child relationships and pathway structure

  • 🧪 Pathway Participants - All molecules participating in pathways

  • ⚗️ Biochemical Reactions - Detailed reaction information

  • 🔗 Protein Interactions - Molecular interactions within pathways

🚀 Quick Start

# Install and build npm install npm run build # Run the server node build/index.js

📋 MCP Client Configuration

Claude Desktop

{ "mcpServers": { "reactome-server": { "command": "node", "args": ["/path/to/reactome-server/build/index.js"] } } }

Other MCP Clients

node /path/to/reactome-server/build/index.js

🛠️ Available Tools

🔍 search_pathways

Search for biological pathways by name, description, or keywords

{ "name": "search_pathways", "arguments": { "query": "cell cycle", // Pathway name, process, or keywords "type": "pathway", // Optional: pathway, reaction, protein, complex, disease "size": 20 // Optional: 1-100 results (default: 20) } }

Example Results:

  • Cell Cycle (R-HSA-1640170) - Cell cycle progression and regulation

  • Cell Cycle Checkpoints (R-HSA-69620) - Quality control mechanisms

  • Mitotic G1-G1/S phases (R-HSA-453279) - G1 phase progression

📊 get_pathway_details

Get comprehensive information about a specific pathway

{ "name": "get_pathway_details", "arguments": { "id": "R-HSA-1640170" // Reactome pathway stable identifier } }

🧬 find_pathways_by_gene

Find all pathways containing a specific gene or protein

{ "name": "find_pathways_by_gene", "arguments": { "gene": "BRCA1", // Gene symbol or UniProt ID "species": "Homo sapiens" // Optional: species (default: Homo sapiens) } }

🦠 find_pathways_by_disease

Find disease-associated pathways and mechanisms

{ "name": "find_pathways_by_disease", "arguments": { "disease": "cancer", // Disease name or DOID identifier "size": 25 // Optional: 1-100 pathways (default: 25) } }

🌲 get_pathway_hierarchy

Get hierarchical structure and parent/child relationships

{ "name": "get_pathway_hierarchy", "arguments": { "id": "R-HSA-1640170" // Reactome pathway stable identifier } }

🧪 get_pathway_participants

Get all molecules (proteins, genes, compounds) in a pathway

{ "name": "get_pathway_participants", "arguments": { "id": "R-HSA-1640170" // Reactome pathway stable identifier } }

⚗️ get_pathway_reactions

Get all biochemical reactions within a pathway

{ "name": "get_pathway_reactions", "arguments": { "id": "R-HSA-1640170" // Reactome pathway stable identifier } }

🔗 get_protein_interactions

Get protein-protein interactions within pathways

{ "name": "get_protein_interactions", "arguments": { "pathwayId": "R-HSA-1640170", // Reactome pathway stable identifier "interactionType": "all" // Optional: protein-protein, regulatory, catalysis, all } }

📚 Resource Templates

Access Reactome data through standardized URIs:

  • reactome://pathway/{id} - Complete pathway information

  • reactome://reaction/{id} - Detailed reaction information

  • reactome://protein/{id} - Protein details and associations

  • reactome://disease/{id} - Disease-associated pathways

  • reactome://search/{query} - Search results

🧪 Real-World Examples

Systems Biology Workflow

# 1. Search for DNA repair pathways {"name": "search_pathways", "arguments": {"query": "DNA repair", "size": 10}} # 2. Get detailed pathway information {"name": "get_pathway_details", "arguments": {"id": "R-HSA-5696394"}} # 3. Find all pathways containing BRCA1 {"name": "find_pathways_by_gene", "arguments": {"gene": "BRCA1"}} # 4. Get pathway participants {"name": "get_pathway_participants", "arguments": {"id": "R-HSA-5696394"}}

Disease Mechanism Research

# 1. Search for cancer-related pathways {"name": "find_pathways_by_disease", "arguments": {"disease": "cancer", "size": 15}} # 2. Get pathway hierarchy for oncogenic signaling {"name": "get_pathway_hierarchy", "arguments": {"id": "R-HSA-5637815"}} # 3. Analyze biochemical reactions {"name": "get_pathway_reactions", "arguments": {"id": "R-HSA-5637815"}}

Drug Discovery Pipeline

# 1. Find pathways for drug target {"name": "find_pathways_by_gene", "arguments": {"gene": "EGFR"}} # 2. Get protein interactions in pathway {"name": "get_protein_interactions", "arguments": {"pathwayId": "R-HSA-177929"}} # 3. Analyze pathway participants {"name": "get_pathway_participants", "arguments": {"id": "R-HSA-177929"}}

🔬 Data Coverage

Reactome provides curated data for:

  • 25,000+ reactions across all major biological processes

  • 14,000+ proteins with detailed functional annotations

  • 2,500+ pathways covering cellular and molecular processes

  • 20+ species including human, mouse, rat, and model organisms

  • Cross-references to UniProt, ChEMBL, Ensembl, and other databases

Key Biological Areas:

  • Signal transduction pathways

  • Metabolic processes and networks

  • Gene regulation and expression

  • Cell cycle and DNA repair

  • Immune system responses

  • Disease mechanisms and drug action

  • Developmental biology processes

🏗️ Architecture

  • TypeScript implementation with robust type safety

  • Reactome Content Service API for efficient data retrieval

  • MCP Protocol compliant JSON-RPC communication

  • Error Handling with comprehensive validation

  • Production Ready with 30s timeouts and proper logging

📊 API Information

  • Base URL: https://reactome.org/ContentService

  • Version: Reactome v79 (latest)

  • Rate Limits: Generous for research use

  • Authentication: None required

  • Format: REST API with JSON responses

🤝 Contributing

  1. Fork the repository

  2. Make your changes

  3. Submit a pull request

Citation

If you use this project in your research or publications, please cite it as follows:

author = {Moudather Chelbi}, title = {Reactome MCP Server}, year = {2025}, howpublished = {https://github.com/Augmented-Nature/Reactome-MCP-Server}, note = {Accessed: 2025-06-29}
Deploy Server
A
security – no known vulnerabilities
A
license - permissive license
A
quality - confirmed to work

How are these scores calculated?

remote-capable server

The server can be hosted and run remotely because it primarily relies on remote services or has no dependency on the local environment.

Tools

Model Context Protocol server for accessing Reactome pathway and systems biology data.

  1. ✅ Verified Features
    1. 🚀 Quick Start
      1. 📋 MCP Client Configuration
        1. Claude Desktop
        2. Other MCP Clients
      2. 🛠️ Available Tools
        1. 🔍 search_pathways
        2. 📊 get_pathway_details
        3. 🧬 find_pathways_by_gene
        4. 🦠 find_pathways_by_disease
        5. 🌲 get_pathway_hierarchy
        6. 🧪 get_pathway_participants
        7. ⚗️ get_pathway_reactions
        8. 🔗 get_protein_interactions
      3. 📚 Resource Templates
        1. 🧪 Real-World Examples
          1. Systems Biology Workflow
          2. Disease Mechanism Research
          3. Drug Discovery Pipeline
        2. 🔬 Data Coverage
          1. 🏗️ Architecture
            1. 📊 API Information
              1. 🤝 Contributing
                1. Citation

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