Nexonco Mcp

by Nexgene-Research

64 stars

473 downloads

Not rated

GitHub

About

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

Details

Author: Nexgene-Research
GitHub stars: 64
Downloads: 473
Categories: Search, AI

- Single tool search_clinical_evidence for querying clinical evidence.
- Returns a formatted report with summary statistics, top evidence, citations, and disclaimer.
- Filter by disease, therapy, molecular profile, phenotype, evidence type, and direction.
- Option to filter only strong evidence (rating > 3).
- Sources and citations included for top evidence entries.
- Designed for research purposes only, not medical advice.

Setting up with Highlight

This MCP is not yet compatible with Highlight’s one-click setup. However, you can still use it with Highlight by following these steps:

Download and install Highlight from highlightai.com/download
Navigate to the plugins tab and select "Add Custom Plugin"
Configure the plugin with the settings below

Plugin Name Nexonco Mcp

Command (node, npx, python, etc.)

Please refer to the README for specific instructions on how to obtain API keys or other required environment variables.
Enable "Start Automatically" if you want the plugin to start when Highlight launches

Setting up with Cursor

Open Cursor's settings
Navigate to the MCP section
Click "Add new Global MCP server"
Copy and paste the configuration below based on your operating system

JSON

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

JSON

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

JSON

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

Setting up with Claude Desktop

Open Claude Desktop's settings
Go to the Integrations tab
Click "Add MCP Server"
Use the configuration below based on your operating system

Note: Make sure Claude Desktop is running before attempting to connect.

JSON

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

JSON

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

JSON

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

Setting up with Windsurf

Open Windsurf's preferences
Go to the Integrations section
Click "Add MCP Integration"
Use the configuration below based on your operating system

JSON

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

JSON

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

JSON

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

Setting up with Cline

Open Cline's settings
Navigate to the Integrations section
Click "Add MCP Server"
Copy and paste the configuration below based on your operating system

Note: Make sure to restart Cline after adding the configuration.

JSON

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

JSON

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

JSON

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

Setting up with Goose

Open Goose's preferences
Go to the Integrations tab
Select "MCP Servers"
Click "Add New Server"
Use the configuration below based on your operating system

JSON

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

JSON

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

JSON

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

From the repository

Install and run using uv or Docker. For MCP integration, you need Claude Desktop. Refer to docs/nanda-server-setup.md and docs/claude-desktop-setup.md for full configuration. Invoke the single tool search_clinical_evidence with optional search filters.

Claude Desktop / Cursor

Paste into your MCP client config file to install this server.

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

McpServers

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

nexonco-mcp-banner

<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>
<br>

</div>

Demo

https://github.com/user-attachments/assets/02129685-5ba5-4b90-89e7-9d4a39986210

Watch full video here:

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: 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
- NANDA: The Internet of AI Agents
- CIViC - Clinical Interpretation of Variants in Cancer

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 - Kutsal Ozkurt (@Goodsea), Nexgene AI

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About

Details

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Setting up with Highlight

From the repository

Claude Desktop / Cursor

McpServers

Demo

Setup

Prerequisites

Setup Guides

Tool List

Input Schema

Output

Sample Usage

Acknowledgements

License

Disclaimer

Contributors

Install

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