Reactome-MCP-Server

Unofficial Reactome MCP Server 🧬

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

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}