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 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
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
- 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:
remote-capable server
The server can be hosted and run remotely because it primarily relies on remote services or has no dependency on the local environment.
Tools
Model Context Protocol server for accessing Reactome pathway and systems biology data.
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