nexonco-mcp 0.1.17
An advanced MCP Server for accessing and analyzing clinical evidence data, with flexible search options to support precision medicine and oncology research.
Requires Python: >=3.11

![nexonco-mcp-banner](https://github.com/user-attachments/assets/c2ec59e8-ff8c-40e1-b66d-17998fe67ecf)

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    <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.
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<div class="title-block" style="text-align: center;" align="center">

  [![PyPI](https://img.shields.io/badge/PyPI-nexonco--mcp-000000.svg?style=for-the-badge&logo=pypi&labelColor=000)](https://pypi.org/project/nexonco-mcp) 
  [![NANDA](https://img.shields.io/badge/NANDA-Nexonco-000000.svg?style=for-the-badge&logo=&labelColor=000)](https://ui.nanda-registry.com/servers/c6284608-6bce-4417-a170-da6c1a117616)
  [![License](https://img.shields.io/badge/License-MIT-000000.svg?style=for-the-badge&logo=github&labelColor=000)](https://github.com/Nexgene-Research/nexonco-mcp/blob/main/LICENSE)
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## Demo

https://github.com/user-attachments/assets/02129685-5ba5-4b90-89e7-9d4a39986210

Watch full video here: [![Youtube](https://img.shields.io/badge/YouTube-red)](https://youtu.be/1Mq8Hcb9V7o?si=jCbhqNabupaRiQWq)

## Setup

### Prerequisites

- [uv](https://github.com/astral-sh/uv#installation) 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="https://github.com/Nexgene-Research/nexonco-mcp/blob/main/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), [Nexgene AI](https://www.nexgene.ai)
- Kutsal Ozkurt (@Goodsea), [Nexgene AI](https://www.nexgene.ai)