Nexonco

Created By

Nexgene-Research8 months ago

A MCP Server for accessing and analyzing clinical evidence data, with flexible search options to support precision medicine and oncology research.

# health

# bio

Overview Content Tools Comments

Content

Nexonco by Nexgene Research is an MCP 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.

Setup

Prerequisites

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:

Summary Statistics:
- Total evidence items
- Average evidence rating
- Top 3 diseases, genes, variants, therapies, and phenotypes (with counts)
Top 10 Evidence Entries:
- Lists the highest-rated evidence items with details like disease, phenotype, gene/variant, therapy, description, type, direction, and rating.
Sources & Citations:
- Citations and URLs for the sources of the top 10 evidence entries.
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

License

This project is licensed under the MIT License - see the LICENSE 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)

Server Config

{
  "mcpServers": {
    "nexonco": {
      "command": "uv",
      "args": [
        "--directory",
        "/full/path/to/nexonco/nexonco",
        "run",
        "server.py"
      ]
    }
  }
}

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