NCBI Entrez MCP Server

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

🚀 Quick Start

Works out of the box - no configuration required!

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

🎯 Features

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

📊 Performance

Configuration	Rate Limit	Performance
Default (No API Key)	3 requests/second	✅ Works out of the box
With API Key	10 requests/second	🚀 3.3x faster

🔑 Optional API Key Setup

For better performance, add your free NCBI API key:

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

See API_KEY_SETUP.md for detailed instructions.

🧪 Testing

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.

Connect to Cloudflare AI Playground

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

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

Connect Claude Desktop to your MCP server

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.

Cloudflare Code Mode Tips

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.