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

📋 MCP Client Configuration

Claude Desktop

Other MCP Clients

🛠️ 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

Disease Mechanism Research

Drug Discovery Pipeline

🔬 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: