A comprehensive MCP server providing access to NCBI APIs, including E-utilities, PubChem, and PMC services for biomedical research data.

Installation

From Source Code

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

Configuration

Claude Desktop

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

Features

Complete NCBI API coverage: E-utilities, PubChem PUG, PMC API
Zero-configuration: Works immediately without any setup
Optional performance boost: Add your free NCBI API key for threefold improvement in request limits
Rate limiting: Built-in compliance with NCBI limits (3/sec → 10/sec with API key)
User-friendly: Designed for both technical and non-technical users

Environment Variables

Optional

NCBI_API_KEY - Optional NCBI API key for improved request limits (10 requests/second versus 3 requests/second)

Notes

The server supports deployment on Cloudflare Workers and can be connected to both Cloudflare AI Playground and Claude Desktop. Performance testing is available through 'node test-rate-limits.js'. For Cloudflare Code Mode, use tool identifiers with underscores instead of hyphens to avoid JavaScript syntax issues.

Entrez MCP Server