NCBI Entrez MCP Server

# 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! ```bash 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: 1. **Get your key**: [NCBI API Key Registration](https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/) (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](API_KEY_SETUP.md) for detailed instructions. ## 🧪 Testing Test your setup and verify rate limits: ```bash 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/mcp`) 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](https://www.npmjs.com/package/mcp-remote). To connect to your MCP server from Claude Desktop, follow [Anthropic's Quickstart](https://modelcontextprotocol.io/quickstart/user) and within Claude Desktop go to Settings > Developer > Edit Config. Update with this configuration: ```json { "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`](docs/codemode.md) for a ready-to-run helper and workflow.