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
🔍 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 informationreactome://reaction/{id} - Detailed reaction informationreactome://protein/{id} - Protein details and associationsreactome://disease/{id} - Disease-associated pathwaysreactome://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
- 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
- Fork the repository
- Make your changes
- 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}