CIViC MCP Server

MCP-supported Chatbot for CIViC users: https://civicdb.org/mcp-chat

Preprint: https://www.biorxiv.org/content/10.1101/2025.10.13.682185v1

This is a Cloudflare Workers-based Model Context Protocol (MCP) server that provides tools for querying the CIViC (Clinical Interpretation of Variants in Cancer) API.

The CIViC database is a crowd-sourced repository of clinical interpretations of cancer variants. This MCP server enables structured queries and data analysis of cancer genomics information through natural language interactions with AI assistants.

Python 3.11.7

pip install -r requirements.txt

Directly Querying the MCP Server

The MCP Server can be called directly from the command line with the optional arguments disease and therapy to get CIViC evidence items:

python MCP_query_evidence.py --mp "EGFR" --disease "Lung Non-small Cell Carcinoma" --therapy "Erlotinib"

Locally Hosting The CIViC MCP Server

We provide an example of doing this with GPT4o-mini. A personal API key is required, update the variable OPENAI_API_KEY in local_hosting/message_MCP_CIViC.py

python local_hosting/message_MCP_CIViC.py --msg "What is the clinical significance of EGFR variants in CIViC?" 

Using With Claude Desktop

https://github.com/user-attachments/assets/5890f79a-e2fc-49f6-b5f4-ef191d07872d

Install Node.js (https://nodejs.org/)

Click "LTS" (Recommended for Most Users) — this gives you Node.js and npx Download and install it like any normal app

Once installed: On Windows: Open “Command Prompt” or “PowerShell” On macOS: Open “Terminal”

Then run:

node -v
npx -v

Confirm that both give versions.

Add this configuration to your claude_desktop_config.json file:

{
  "mcpServers": {
    "civic-mcp-server": {
      "command": "npx",
      "args": [
        "mcp-remote",
        "https://civic-mcp-server.larscivic.workers.dev/mcp"
      ]
    }
  }
}

Alternativly, the MCP server can be added as a connector (currently limited to paid Claude users). For more details visit https://support.claude.com/en/articles/11176164-pre-built-web-connectors-using-remote-mcp

Usage

Once configured, restart Claude Desktop. The server provides two main tools:

1. get_variant_evidence: Return up to 50 evidence items for a CIViC molecular profile
2. get_variant_assertions: Return CIViC assertions for a molecular profile

Evaluation Scripts

All evaluation files are located in eval_QA_experiment/

License

MIT License with Academic Citation Requirement - see LICENSE.md