{
  "markdown": "# 🧬 GWAS-MCP: Bioinformatics MCP Server\n\n[![PyPI version](https://badge.fury.io/py/gwas-mcp.svg)](https://badge.fury.io/py/gwas-mcp)\n[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n[![MCP](https://img.shields.io/badge/MCP-Compatible-blue)](https://modelcontextprotocol.io)\n\n<!-- mcp-name: io.github.zaeyasa/gwas-mcp -->\n\nA 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.\n\n<p align=\"center\">\n  <img src=\"https://img.shields.io/badge/Tools-30+-green\" alt=\"30+ Tools\">\n  <img src=\"https://img.shields.io/badge/Databases-12+-blue\" alt=\"12+ Databases\">\n  <img src=\"https://img.shields.io/badge/Python-3.10+-blue\" alt=\"Python 3.10+\">\n</p>\n\n---\n\n## ✨ Features\n\n### 🔬 Protein & Gene Lookup\n- **UniProt** - Search proteins by name, gene, or ID\n- **Ensembl** - Gene information and variant details\n- **NCBI Gene** - Comprehensive gene database\n\n### 🧪 Clinical & Variants\n- **ClinVar** - Clinical variant interpretations (pathogenic/benign)\n- **GWAS Catalog** - Genome-wide association studies\n- **GTEx** - Expression quantitative trait loci (eQTL)\n\n### 🔗 Protein Interactions & Networks\n- **STRING** - Protein-protein interactions\n- **InterPro** - Protein domains and families\n\n### 🏗️ Structures & Pathways\n- **AlphaFold** - AI-predicted protein structures\n- **PDB** - Experimental 3D structures\n- **KEGG** - Metabolic and signaling pathways\n\n### 💊 Drug Discovery\n- **Open Targets** - Drug target validation & disease associations\n- **PharmGKB** - Pharmacogenomics & drug-gene interactions\n\n### 🏥 Genetic Diseases\n- **OMIM** - Online Mendelian Inheritance in Man\n\n---\n\n## 🚀 Quick Start\n\n### Installation\n\n```bash\npip install gwas-mcp\n```\n\n### Claude Desktop Configuration\n\nAdd to your `claude_desktop_config.json`:\n\n```json\n{\n  \"mcpServers\": {\n    \"gwas-bioinformatics\": {\n      \"command\": \"python\",\n      \"args\": [\"-m\", \"gwas_mcp.server\"]\n    }\n  }\n}\n```\n\n**Config file location:**\n- Windows: `%APPDATA%\\Claude\\claude_desktop_config.json`\n- macOS: `~/Library/Application Support/Claude/claude_desktop_config.json`\n- Linux: `~/.config/Claude/claude_desktop_config.json`\n\n### Restart Claude Desktop\n\nAfter adding the configuration, restart Claude Desktop to load the MCP server.\n\n---\n\n## 🛠️ Available Tools\n\n### Protein & Gene Tools\n\n| Tool | Description |\n|------|-------------|\n| `search_uniprot` | Search UniProt by protein name, gene, or ID |\n| `get_protein_details` | Get detailed protein info (function, domains, GO terms) |\n| `search_ncbi_gene` | Search NCBI Gene database |\n| `search_ensembl_gene` | Get gene location and details from Ensembl |\n| `get_variant_info` | Get SNP/variant info by rsID |\n| `get_interpro_domains` | Get protein domain information |\n\n### Clinical & Variant Tools\n\n| Tool | Description |\n|------|-------------|\n| `search_clinvar` | Search ClinVar for clinical variants |\n| `get_clinvar_variant` | Get clinical interpretation for a variant |\n| `annotate_snps` | Annotate SNPs with functional consequences |\n| `query_gwas_catalog` | Query GWAS Catalog for associations |\n| `get_eqtl_data` | Get eQTL data from GTEx |\n\n### Protein Interaction Tools\n\n| Tool | Description |\n|------|-------------|\n| `get_protein_interactions` | Find interacting proteins (STRING) |\n| `get_interaction_network` | Get network between multiple proteins |\n| `get_functional_enrichment` | Pathway/GO enrichment analysis |\n\n### Structure & Pathway Tools\n\n| Tool | Description |\n|------|-------------|\n| `get_alphafold_structure` | Get AI-predicted structure |\n| `search_alphafold` | Search AlphaFold database |\n| `search_pdb_structures` | Search PDB for 3D structures |\n| `get_pdb_structure` | Get PDB structure details |\n| `search_kegg_pathway` | Search KEGG pathways |\n| `get_kegg_pathway` | Get pathway genes and details |\n| `get_gene_pathways` | Find pathways for a gene |\n\n### Drug Discovery Tools\n\n| Tool | Description |\n|------|-------------|\n| `get_drug_targets` | Find drugs targeting a gene (Open Targets) |\n| `get_disease_associations` | Get disease associations with scores |\n| `search_open_targets` | Search genes, diseases, or drugs |\n| `search_pharmgkb` | Search PharmGKB database |\n| `get_drug_gene_interactions` | Get drug-gene interactions |\n\n### Genetic Disease Tools\n\n| Tool | Description |\n|------|-------------|\n| `search_omim` | Search OMIM for genetic diseases |\n| `get_gene_diseases` | Get all diseases for a gene |\n\n---\n\n## 💬 Example Prompts\n\nOnce configured, ask Claude naturally:\n\n### Protein & Gene Queries\n> \"Get information about the BRCA1 gene\"\n> \n> \"Search UniProt for hemoglobin\"\n> \n> \"What protein has UniProt ID P53_HUMAN?\"\n\n### Clinical Variants\n> \"Is the BRCA1 variant rs80357906 pathogenic?\"\n> \n> \"Search ClinVar for TP53 variants\"\n\n### Protein Interactions\n> \"What proteins interact with TP53?\"\n> \n> \"Find functional enrichment for BRCA1, ATM, and CHEK2\"\n\n### Structures & Pathways\n> \"Get the AlphaFold structure for TP53\"\n> \n> \"What pathways is BRCA1 involved in?\"\n> \n> \"Search PDB for insulin structures\"\n\n### Drug Discovery\n> \"What drugs target EGFR?\"\n> \n> \"What diseases is BRAF associated with?\"\n\n### Genetic Diseases\n> \"Search OMIM for cystic fibrosis\"\n> \n> \"What diseases are linked to the CFTR gene?\"\n\n---\n\n## ⚡ Performance Features\n\n- **Smart Caching** - API responses cached for 1 hour to improve speed\n- **Async Operations** - All API calls are non-blocking\n- **Error Handling** - Graceful handling of API failures\n\n---\n\n## 🔧 Development\n\n### From Source\n\n```bash\n# Clone the repository\ngit clone https://github.com/zaeyasa/gwas-mcp.git\ncd gwas-mcp\n\n# Install dependencies\npip install -e .\n\n# Run the server\npython -m gwas_mcp.server\n```\n\n### Project Structure\n\n```\ngwas-mcp/\n├── src/\n│   └── gwas_mcp/\n│       ├── server.py           # Main MCP server\n│       ├── tools/\n│       │   ├── protein_tools.py     # UniProt, NCBI, Ensembl\n│       │   ├── clinical_tools.py    # ClinVar, STRING\n│       │   ├── structure_tools.py   # PDB, KEGG, PharmGKB\n│       │   └── advanced_tools.py    # AlphaFold, Open Targets, OMIM\n│       └── resources/\n│           └── db_resources.py      # Database resources\n├── pyproject.toml\n├── README.md\n└── LICENSE\n```\n\n---\n\n## 📊 Supported Databases\n\n| Database | Type | Description |\n|----------|------|-------------|\n| [UniProt](https://www.uniprot.org/) | Protein | Protein sequences and annotations |\n| [Ensembl](https://www.ensembl.org/) | Gene/Variant | Genome browser and variant data |\n| [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/) | Gene | Gene information database |\n| [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/) | Clinical | Clinical variant interpretations |\n| [GWAS Catalog](https://www.ebi.ac.uk/gwas/) | GWAS | Genome-wide association studies |\n| [GTEx](https://gtexportal.org/) | Expression | Expression QTL data |\n| [STRING](https://string-db.org/) | Interactions | Protein-protein interactions |\n| [InterPro](https://www.ebi.ac.uk/interpro/) | Domains | Protein families and domains |\n| [AlphaFold](https://alphafold.ebi.ac.uk/) | Structure | AI-predicted structures |\n| [PDB](https://www.rcsb.org/) | Structure | Experimental 3D structures |\n| [KEGG](https://www.kegg.jp/) | Pathways | Metabolic and signaling pathways |\n| [Open Targets](https://platform.opentargets.org/) | Drug Discovery | Drug targets and disease associations |\n| [PharmGKB](https://www.pharmgkb.org/) | Pharmacogenomics | Drug-gene interactions |\n| [OMIM](https://omim.org/) | Diseases | Genetic disease database |\n\n---\n\n## 🤝 Contributing\n\nContributions are welcome! Please feel free to submit a Pull Request.\n\n1. Fork the repository\n2. Create your feature branch (`git checkout -b feature/amazing-feature`)\n3. Commit your changes (`git commit -m 'Add amazing feature'`)\n4. Push to the branch (`git push origin feature/amazing-feature`)\n5. Open a Pull Request\n\n---\n\n## 📄 License\n\nThis project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.\n\n---\n\n## 🙏 Acknowledgments\n\n- [Model Context Protocol](https://modelcontextprotocol.io/) - The MCP specification\n- [Anthropic](https://www.anthropic.com/) - Claude AI and MCP development\n- All the amazing bioinformatics databases that make this possible\n\n---\n\n## 📬 Contact\n\n- GitHub: [@zaeyasa](https://github.com/zaeyasa)\n\n---\n\n<p align=\"center\">Made with ❤️ for the bioinformatics community</p>\n",
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