Skip to main content
Glama

Reactome MCP Server

by Augmented-Nature
GitHub
JavaScript
MIT License
5
OverviewInspectNewSchemaRelated ServersReviewsScore
Need Help?View Source CodeReport Issue

Logo

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

{ "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 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

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}

This server cannot be installed

-
security - not tested
A
license - permissive license
-
quality - not tested

How are these scores calculated?

Model Context Protocol server for accessing Reactome pathway and systems biology data.

  1. ✅ Verified Features
    1. 🚀 Quick Start
      1. 📋 MCP Client Configuration
        1. Claude Desktop
        2. Other MCP Clients
      2. 🛠️ Available Tools
        1. 🔍 search_pathways
        2. 📊 get_pathway_details
        3. 🧬 find_pathways_by_gene
        4. 🦠 find_pathways_by_disease
        5. 🌲 get_pathway_hierarchy
        6. 🧪 get_pathway_participants
        7. ⚗️ get_pathway_reactions
        8. 🔗 get_protein_interactions
      3. 📚 Resource Templates
        1. 🧪 Real-World Examples
          1. Systems Biology Workflow
          2. Disease Mechanism Research
          3. Drug Discovery Pipeline
        2. 🔬 Data Coverage
          1. 🏗️ Architecture
            1. 📊 API Information
              1. 🤝 Contributing
                1. Citation

                  Related MCP Servers

                  • MCP Server Fetch TypeScript

                    tatn
                    A
                    security
                    A
                    license
                    A
                    quality
                    A Model Context Protocol server that provides web content fetching and conversion capabilities.
                    Last updated -
                    4
                    89
                    2
                    JavaScript
                    MIT License
                    • Apple

                  • Biomart MCP

                    jzinno
                    A
                    security
                    A
                    license
                    A
                    quality
                    A Model Context Protocol server that interfaces with Biomart databases, allowing models to discover biological datasets, explore attributes/filters, retrieve biological data, and translate between different biological identifiers.
                    Last updated -
                    8
                    5
                    Python
                    MIT License
                    • Apple
                    • Linux

                  • MCP Boilerplate

                    iamsrikanthnani
                    -
                    security
                    A
                    license
                    -
                    quality
                    A server that implements the Model Context Protocol, providing a standardized way to connect AI models to different data sources and tools.
                    Last updated -
                    3
                    5
                    TypeScript
                    MIT License

                  • Unofficial PubChem MCP Server

                    Augmented-Nature
                    A
                    security
                    A
                    license
                    A
                    quality
                    A comprehensive Model Context Protocol server providing access to over 110 million chemical compounds with extensive molecular properties, bioassay data, and chemical informatics tools from the PubChem database.
                    Last updated -
                    30
                    12
                    JavaScript
                    MIT License

                  View all related MCP servers

                  New MCP Servers

                  MCP directory API

                  We provide all the information about MCP servers via our MCP API.

                  curl -X GET 'https://glama.ai/api/mcp/v1/servers/Augmented-Nature/Reactome-MCP-Server'

                  If you have feedback or need assistance with the MCP directory API, please join our Discord server