nexonco-mcp

 <div class="title-block" style="text-align: center;" align="center"> <b>Nexonco</b> by <a href="https://www.nexgene.ai">Nexgene Research</a> is an <a href="https://github.com/modelcontextprotocol">MCP</a> server for accessing clinical evidence from the CIViC (Clinical Interpretation of Variants in Cancer) database. It enables fast, flexible search across variants, diseases, drugs, and phenotypes to support precision oncology. </div> ## Setup ### Prerequisites - [uv](https://github.com/astral-sh/uv) or Docker - Claude Desktop (for MCP integration) ### Setup Guides For detailed setup instructions, refer to the following documentation: - **NANDA Host Setup** See `docs/nanda-server-setup.md` for backend configuration and local registration of the NANDA Server. - **Claude Desktop Setup** See `docs/claude-desktop-setup.md` for guidance on configuring the local development environment and MCP integration. These guides include all required steps, environment configurations, and usage notes to get up and running. ## Tool List `search_clinical_evidence`: A MCP tool for querying clinical evidence data that returns formatted reports. ### Input Schema The tool accepts the following optional parameters: - **`disease_name` (str)**: Filter by disease (e.g., "Lung Non-small Cell Carcinoma"). - **`therapy_name` (str)**: Filter by therapy or drug (e.g., "Cetuximab"). - **`molecular_profile_name` (str)**: Filter by gene or variant (e.g., "EGFR L858R"). - **`phenotype_name` (str)**: Filter by phenotype (e.g., "Chest Pain"). - **`evidence_type` (str)**: Filter by evidence type (e.g., "PREDICTIVE", "DIAGNOSTIC"). - **`evidence_direction` (str)**: Filter by evidence direction (e.g., "SUPPORTS"). - **`filter_strong_evidence` (bool)**: If `True`, only includes evidence with a rating > 3 (max 5). ### Output The tool returns a formatted string with four sections: 1. **Summary Statistics**: - Total evidence items - Average evidence rating - Top 3 diseases, genes, variants, therapies, and phenotypes (with counts) 2. **Top 10 Evidence Entries**: - Lists the highest-rated evidence items with details like disease, phenotype, gene/variant, therapy, description, type, direction, and rating. 3. **Sources & Citations**: - Citations and URLs for the sources of the top 10 evidence entries. 4. **Disclaimer**: - A note stating the tool is for research purposes only, not medical advice. ## Sample Usage - "Find predictive evidence for colorectal cancer therapies involving KRAS mutations." - "Are there studies on Imatinib for leukemia?" - "What therapies are linked to pancreatic cancer evidence?" ## Acknowledgements - [Model Context Protocol](https://github.com/modelcontextprotocol/python-sdk) - [NANDA: The Internet of AI Agents](https://nanda.media.mit.edu/) - [CIViC - Clinical Interpretation of Variants in Cancer](https://civicdb.org) ## License This project is licensed under the MIT License - see the <a href="LICENSE">LICENSE</a> file for details. ## Disclaimer ⚠️ This tool is intended exclusively for research purposes. It is not a substitute for professional medical advice, diagnosis, or treatment. ## Contributors - Obada Qasem (@obadaqasem) - Kutsal Ozkurt (@Goodsea)