NCBI Entrez MCP Server

Access NCBI's suite of APIs, including E-utilities, BLAST, PubChem, and PMC services.

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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

ConfigurationRate LimitPerformance
Default (No API Key)3 requests/second✅ Works out of the box
With API Key10 requests/second🚀 3.3x faster

🔑 Optional API Key Setup

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.

🧪 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:

  1. Go to https://playground.ai.cloudflare.com/
  2. Enter your deployed MCP server URL (remote-mcp-server-authless.<your-account>.workers.dev/sse)
  3. 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/sse"  // or remote-mcp-server-authless.your-account.workers.dev/sse
      ]
    }
  }
}

Restart Claude and you should see the tools become available.

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