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 searching across variants, diseases, drugs, and phenotypes to support precision oncology research and applications.

Installation

Prerequisites

Before installing Nexonco, you'll need:

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

Installation Options

Using PyPI

The simplest way to install Nexonco is via PyPI:

uv pip install nexonco-mcp

Using Docker

If you prefer Docker, you can pull and run the Nexonco container (refer to the NANDA server setup documentation for details).

Configuration

NANDA Server Setup

To configure the backend and register with NANDA Server:

1. Install the required packages
2. Set up environment variables for authentication
3. Register your local server with NANDA

Claude Desktop Integration

To integrate with Claude Desktop:

1. Install Claude Desktop
2. Configure MCP integration settings
3. Connect Claude Desktop to your local Nexonco server

Using the Tool

Nexonco provides a primary tool called search_clinical_evidence that allows you to query clinical evidence data.

Tool Parameters

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 Format

The tool returns a formatted report with four main sections:

1. Summary Statistics - Provides overview counts and averages
2. Top 10 Evidence Entries - Lists the highest-rated evidence with details
3. Sources & Citations - References for the evidence
4. Disclaimer - Research-only usage notice

Example Queries

Here are some example questions you can ask:

• "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 Disclaimer

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

How to add this MCP server to 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 > MCP and click "Add new global MCP server".

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

{
    "mcpServers": {
        "cursor-rules-mcp": {
            "command": "npx",
            "args": [
                "-y",
                "cursor-rules-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 explictly ask the agent to use the tool by mentioning the tool name and describing what the function does.