🧬 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

Terminal

pip install gwas-mcp

Claude Desktop Configuration

Add to your claude_desktop_config.json:

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

bash

# 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

Code

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