MCP server for working with the CIViC (Clinical Interpretation of Variants in Cancer) database, enabling structured queries and analysis of cancer genomics and clinical variant interpretation information through GraphQL and SQL.

Installation

Deploy to Cloudflare Workers

git clone <repository-url>
cd civic-mcp-server
npm install
npm run deploy

Configuration

Claude Desktop

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

Available Tools

Tool	Description
civic_graphql_query	Execute GraphQL queries against the CIViC API
civic_query_sql	Query pre-processed data using SQL

Features

• GraphQL to SQL conversion: Automatically transforms CIViC API responses into structured SQLite tables
• Efficient data storage: Uses Cloudflare Durable Objects with SQLite for intermediate storage and queries
• Smart response handling: Optimizes performance by bypassing intermediate storage for small responses, errors, and schema queries
• Two-stage pipeline: GraphQL queries and SQL analysis of intermediate data
• Dataset management: Helper endpoints for managing intermediate datasets
• Three MCP prompts: get-variant-evidence, get-variant-assertions, get-variant-data with reliable GraphQL generation

Usage Examples

What are the latest BRAF mutation data?

Show all therapeutic interpretations for lung cancer variants

Find genes with the most data in the CIViC database

/get-variant-evidence molecularProfileName:"TP53 Mutation" diseaseName:"Lung Adenocarcinoma" evidenceType:"PROGNOSTIC" first:"200"

/get-variant-assertions molecularProfileName:"TPM3-NTRK1 Fusion" therapyName:"Larotrectinib" status:"ALL"

Notes

Implements MCP specification 2025-06-18. Requires deployment to Cloudflare Workers and provides dataset management endpoints at /datasets. Uses intelligent response handling to optimize context usage, storing large results in SQLite and returning small responses directly.