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.