Content
# Unofficial Reactome MCP Server 🧬
Model Context Protocol server for accessing Reactome pathway and systems biology data.
[](https://reactome.org/)
Developed by [Augmented Nature](https://augmentednature.ai) - 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**
```bash
# Install and build
npm install
npm run build
# Run the server
node build/index.js
```
## 📋 **MCP Client Configuration**
### Claude Desktop
```json
{
"mcpServers": {
"reactome-server": {
"command": "node",
"args": ["/path/to/reactome-server/build/index.js"]
}
}
}
```
### Other MCP Clients
```bash
node /path/to/reactome-server/build/index.js
```
## 🛠️ **Available Tools**
### 🔍 `search_pathways`
**Search for biological pathways by name, description, or keywords**
```json
{
"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**
```json
{
"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**
```json
{
"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**
```json
{
"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**
```json
{
"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**
```json
{
"name": "get_pathway_participants",
"arguments": {
"id": "R-HSA-1640170" // Reactome pathway stable identifier
}
}
```
### ⚗️ `get_pathway_reactions`
**Get all biochemical reactions within a pathway**
```json
{
"name": "get_pathway_reactions",
"arguments": {
"id": "R-HSA-1640170" // Reactome pathway stable identifier
}
}
```
### 🔗 `get_protein_interactions`
**Get protein-protein interactions within pathways**
```json
{
"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
```bash
# 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
```bash
# 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
```bash
# 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:
```bibtex @misc{reactomemcp2025,
author = {Moudather Chelbi},
title = {Reactome MCP Server},
year = {2025},
howpublished = {https://github.com/Augmented-Nature/Reactome-MCP-Server},
note = {Accessed: 2025-06-29}
