What is Reactome Mcp Server

Reactome-MCP-Server is a Model Context Protocol server designed to provide access to Reactome pathway and systems biology data, facilitating the exploration of biological pathways and their components.

Use cases

Use cases include searching for specific biological pathways, analyzing the role of genes in pathways, studying disease mechanisms, and exploring molecular interactions within biological systems.

How to use

To use Reactome-MCP-Server, install the necessary packages using npm, build the project, and run the server with the provided commands. Configuration for different MCP clients is also available.

Key features

Key features include: pathway search by name or keywords, detailed pathway information, gene-to-pathways mapping, disease-associated pathways, pathway hierarchy visualization, participant molecules in pathways, biochemical reaction details, and protein interactions.

Where to use

Reactome-MCP-Server is applicable in fields such as bioinformatics, systems biology, and medical research, where understanding biological pathways is crucial.

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

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

🧬 find_pathways_by_gene

Find all pathways containing a specific gene or protein

🦠 find_pathways_by_disease

Find disease-associated pathways and mechanisms

🌲 get_pathway_hierarchy

Get hierarchical structure and parent/child relationships

🧪 get_pathway_participants

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

⚗️ get_pathway_reactions

Get all biochemical reactions within a pathway

🔗 get_protein_interactions

Get protein-protein interactions within pathways

📚 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