A comprehensive Model Context Protocol (MCP) server providing access to NCBI's APIs including E-utilities, PubChem, and PMC services.

Works out of the box - no configuration required!

git clone <this-repo>
cd entrez-mcp-server
npm install
npm start

• Complete NCBI API Coverage: E-utilities, PubChem PUG, PMC APIs
• No Setup Required: Works immediately without any configuration
• Optional Performance Boost: Add your free NCBI API key for 3x better rate limits
• Rate Limiting: Built-in respect for NCBI rate limits (3/sec → 10/sec with API key)
• User-Friendly: Designed for both technical and non-technical users

For better performance, add your free NCBI API key:

1. Get your key: NCBI API Key Registration (takes 30 seconds)
2. Set environment variable: export NCBI_API_KEY="your_key_here"
3. Test it works: node test-rate-limits.js

See API_KEY_SETUP.md for detailed instructions.

Test your setup and verify rate limits:

node test-rate-limits.js

This will test both authenticated and unauthenticated scenarios and verify your API key is working correctly.

You can connect to your MCP server from the Cloudflare AI Playground, which is a remote MCP client:

1. Go to https://playground.ai.cloudflare.com/
2. Enter your deployed MCP server URL (remote-mcp-server-authless.<your-account>.workers.dev/mcp)
3. You can now use your MCP tools directly from the playground!

You can also connect to your remote MCP server from local MCP clients, by using the mcp-remote proxy.

To connect to your MCP server from Claude Desktop, follow Anthropic's Quickstart and within Claude Desktop go to Settings > Developer > Edit Config.

Update with this configuration:

{
  "mcpServers": {
    "calculator": {
      "command": "npx",
      "args": [
        "mcp-remote",
        "http://localhost:8787/mcp"  // or remote-mcp-server-authless.your-account.workers.dev/mcp
      ]
    }
  }
}

Restart Claude and you should see the tools become available.

When running this MCP server from Cloudflare's Code Mode experiments, prefer the underscore tool IDs (for example tool_Z1YjsltQ_entrez_query). Legacy hyphenated aliases (…_entrez-query) are still available for backward compatibility, but JavaScript treats codemode.tool_Z1YjsltQ_entrez-query as subtraction and throws ReferenceError. Either stick to the underscore versions or call the hyphenated aliases with bracket notation (codemode["tool_Z1YjsltQ_entrez-query"](...)). See docs/codemode.md for a ready-to-run helper and workflow.