🧬 GWAS-MCP: Bioinformatics MCP Server
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.
✨ 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
| Tool | Description |
|---|---|
search_uniprot | Search UniProt by protein name, gene, or ID |
get_protein_details | Get detailed protein info (function, domains, GO terms) |
search_ncbi_gene | Search NCBI Gene database |
search_ensembl_gene | Get gene location and details from Ensembl |
get_variant_info | Get SNP/variant info by rsID |
get_interpro_domains | Get protein domain information |
Clinical & Variant Tools
| Tool | Description |
|---|---|
search_clinvar | Search ClinVar for clinical variants |
get_clinvar_variant | Get clinical interpretation for a variant |
annotate_snps | Annotate SNPs with functional consequences |
query_gwas_catalog | Query GWAS Catalog for associations |
get_eqtl_data | Get eQTL data from GTEx |
Protein Interaction Tools
| Tool | Description |
|---|---|
get_protein_interactions | Find interacting proteins (STRING) |
get_interaction_network | Get network between multiple proteins |
get_functional_enrichment | Pathway/GO enrichment analysis |
Structure & Pathway Tools
| Tool | Description |
|---|---|
get_alphafold_structure | Get AI-predicted structure |
search_alphafold | Search AlphaFold database |
search_pdb_structures | Search PDB for 3D structures |
get_pdb_structure | Get PDB structure details |
search_kegg_pathway | Search KEGG pathways |
get_kegg_pathway | Get pathway genes and details |
get_gene_pathways | Find pathways for a gene |
Drug Discovery Tools
| Tool | Description |
|---|---|
get_drug_targets | Find drugs targeting a gene (Open Targets) |
get_disease_associations | Get disease associations with scores |
search_open_targets | Search genes, diseases, or drugs |
search_pharmgkb | Search PharmGKB database |
get_drug_gene_interactions | Get drug-gene interactions |
Genetic Disease Tools
| Tool | Description |
|---|---|
search_omim | Search OMIM for genetic diseases |
get_gene_diseases | Get all diseases for a gene |
💬 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
| Database | Type | Description |
|---|---|---|
| UniProt | Protein | Protein sequences and annotations |
| Ensembl | Gene/Variant | Genome browser and variant data |
| NCBI Gene | Gene | Gene information database |
| ClinVar | Clinical | Clinical variant interpretations |
| GWAS Catalog | GWAS | Genome-wide association studies |
| GTEx | Expression | Expression QTL data |
| STRING | Interactions | Protein-protein interactions |
| InterPro | Domains | Protein families and domains |
| AlphaFold | Structure | AI-predicted structures |
| PDB | Structure | Experimental 3D structures |
| KEGG | Pathways | Metabolic and signaling pathways |
| Open Targets | Drug Discovery | Drug targets and disease associations |
| PharmGKB | Pharmacogenomics | Drug-gene interactions |
| OMIM | Diseases | Genetic disease database |
🤝 Contributing
Contributions are welcome! Please feel free to submit a Pull Request.
- Fork the repository
- Create your feature branch (
git checkout -b feature/amazing-feature) - Commit your changes (
git commit -m 'Add amazing feature') - Push to the branch (
git push origin feature/amazing-feature) - 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
Made with ❤️ for the bioinformatics community