NexOnco (CIViC Precision Oncology) MCP server

Nexonco by Nexgene Research is an MCP server that provides access to 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 research.

Installation

Prerequisites

Before installing Nexonco, you need to have either:

• uv installed, or
• Docker installed
• Claude Desktop (for MCP integration)

Installation Methods

Using PyPI

The simplest way to install Nexonco is via PyPI:

pip install nexonco-mcp

Using Docker

Alternatively, you can run Nexonco in a Docker container (specific Docker commands not provided in the original README).

Configuration

NANDA Server Integration

To set up Nexonco as a NANDA server:

1. Install the required dependencies
2. Configure your environment variables (specific details would be in the docs folder of the original repository)
3. Register the server locally with NANDA

Claude Desktop Integration

To integrate with Claude Desktop:

1. Ensure Claude Desktop is installed
2. Configure the MCP integration
3. Connect Claude Desktop to your local Nexonco server

Usage

Nexonco provides a clinical evidence search tool that can be accessed through the MCP protocol.

Available Tool

search_clinical_evidence: Queries clinical evidence data and returns formatted reports.

Parameters

The search tool accepts these 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 Format

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
   • Includes 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

Example Queries

You can use the following query examples with Claude Desktop:

• "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?"

Important Note

⚠️ This tool is intended exclusively for research purposes. It is not a substitute for professional medical advice, diagnosis, or treatment.

How to install this MCP server

For Claude Code

To add this MCP server to Claude Code, run this command in your terminal:

claude mcp add-json "nexonco-mcp" '{"command":"npx","args":["-y","nexonco-mcp"]}'

See the official Claude Code MCP documentation for more details.

For Cursor

There are two ways to add an MCP server to Cursor. The most common way is to add the server globally in the ~/.cursor/mcp.json file so that it is available in all of your projects.

If you only need the server in a single project, you can add it to the project instead by creating or adding it to the .cursor/mcp.json file.

Adding an MCP server to Cursor globally

To add a global MCP server go to Cursor Settings > Tools & Integrations and click "New MCP Server".

When you click that button the ~/.cursor/mcp.json file will be opened and you can add your server like this:

{
    "mcpServers": {
        "nexonco-mcp": {
            "command": "npx",
            "args": [
                "-y",
                "nexonco-mcp"
            ]
        }
    }
}

Adding an MCP server to a project

To add an MCP server to a project you can create a new .cursor/mcp.json file or add it to the existing one. This will look exactly the same as the global MCP server example above.

How to use the MCP server

Once the server is installed, you might need to head back to Settings > MCP and click the refresh button.

The Cursor agent will then be able to see the available tools the added MCP server has available and will call them when it needs to.

You can also explicitly ask the agent to use the tool by mentioning the tool name and describing what the function does.

For Claude Desktop

To add this MCP server to Claude Desktop:

1. Find your configuration file:

• macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
• Windows: %APPDATA%\Claude\claude_desktop_config.json
• Linux: ~/.config/Claude/claude_desktop_config.json

2. Add this to your configuration file:

{
    "mcpServers": {
        "nexonco-mcp": {
            "command": "npx",
            "args": [
                "-y",
                "nexonco-mcp"
            ]
        }
    }
}

3. Restart Claude Desktop for the changes to take effect