🧬 GWAS-MCP: Bioinformatics MCP Server

<!-- mcp-name: io.github.zaeyasa/gwas-mcp -->

A powerful Model Context Protocol (MCP) server for GWAS and bioinformatics research. Seamlessly integrates with Claude Desktop and other MCP clients to provide AI-powered access to major biological databases.

<p align="center"> <img src="https://img.shields.io/badge/Tools-30+-green" alt="30+ Tools"> <img src="https://img.shields.io/badge/Databases-12+-blue" alt="12+ Databases"> <img src="https://img.shields.io/badge/Python-3.10+-blue" alt="Python 3.10+"> </p>

✨ Features

🔬 Protein & Gene Lookup

• UniProt - Search proteins by name, gene, or ID
• Ensembl - Gene information and variant details
• NCBI Gene - Comprehensive gene database

🧪 Clinical & Variants

• ClinVar - Clinical variant interpretations (pathogenic/benign)
• GWAS Catalog - Genome-wide association studies
• GTEx - Expression quantitative trait loci (eQTL)

🔗 Protein Interactions & Networks

• STRING - Protein-protein interactions
• InterPro - Protein domains and families

🏗️ Structures & Pathways

• AlphaFold - AI-predicted protein structures
• PDB - Experimental 3D structures
• KEGG - Metabolic and signaling pathways

💊 Drug Discovery

• Open Targets - Drug target validation & disease associations
• PharmGKB - Pharmacogenomics & drug-gene interactions

🏥 Genetic Diseases

• OMIM - Online Mendelian Inheritance in Man

🚀 Quick Start

Installation

pip install gwas-mcp

Claude Desktop Configuration

Add to your claude_desktop_config.json:

{
  "mcpServers": {
    "gwas-bioinformatics": {
      "command": "python",
      "args": ["-m", "gwas_mcp.server"]
    }
  }
}

Config file location:

• Windows: %APPDATA%\Claude\claude_desktop_config.json
• macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
• Linux: ~/.config/Claude/claude_desktop_config.json

Restart Claude Desktop

After adding the configuration, restart Claude Desktop to load the MCP server.

🛠️ Available Tools

Protein & Gene Tools

Clinical & Variant Tools

Protein Interaction Tools

Structure & Pathway Tools

Drug Discovery Tools

Genetic Disease Tools

💬 Example Prompts

Once configured, ask Claude naturally:

Protein & Gene Queries

"Get information about the BRCA1 gene"

>

"Search UniProt for hemoglobin"

>

"What protein has UniProt ID P53_HUMAN?"

Clinical Variants

"Is the BRCA1 variant rs80357906 pathogenic?"

>

"Search ClinVar for TP53 variants"

Protein Interactions

"What proteins interact with TP53?"

>

"Find functional enrichment for BRCA1, ATM, and CHEK2"

Structures & Pathways

"Get the AlphaFold structure for TP53"

>

"What pathways is BRCA1 involved in?"

>

"Search PDB for insulin structures"

Drug Discovery

"What drugs target EGFR?"

>

"What diseases is BRAF associated with?"

Genetic Diseases

"Search OMIM for cystic fibrosis"

>

"What diseases are linked to the CFTR gene?"

⚡ Performance Features

• Smart Caching - API responses cached for 1 hour to improve speed
• Async Operations - All API calls are non-blocking
• Error Handling - Graceful handling of API failures

🔧 Development

From Source

# Clone the repository
git clone https://github.com/zaeyasa/gwas-mcp.git
cd gwas-mcp

# Install dependencies
pip install -e .

# Run the server
python -m gwas_mcp.server

Project Structure

gwas-mcp/
├── src/
│   └── gwas_mcp/
│       ├── server.py           # Main MCP server
│       ├── tools/
│       │   ├── protein_tools.py     # UniProt, NCBI, Ensembl
│       │   ├── clinical_tools.py    # ClinVar, STRING
│       │   ├── structure_tools.py   # PDB, KEGG, PharmGKB
│       │   └── advanced_tools.py    # AlphaFold, Open Targets, OMIM
│       └── resources/
│           └── db_resources.py      # Database resources
├── pyproject.toml
├── README.md
└── LICENSE

📊 Supported Databases

🤝 Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

1. Fork the repository
2. Create your feature branch (git checkout -b feature/amazing-feature)
3. Commit your changes (git commit -m 'Add amazing feature')
4. Push to the branch (git push origin feature/amazing-feature)
5. Open a Pull Request

📄 License

This project is licensed under the MIT License - see the LICENSE file for details.

🙏 Acknowledgments

• Model Context Protocol - The MCP specification
• Anthropic - Claude AI and MCP development
• All the amazing bioinformatics databases that make this possible

📬 Contact

• GitHub: @zaeyasa

<p align="center">Made with ❤️ for the bioinformatics community</p>