PubMed Research Access MCP Server

Overview

PubMed Research Access is an MCP server that connects to the PubMed database through the NCBI Entrez API, allowing AI assistants to search and retrieve medical research papers. This tool is particularly useful for research tasks requiring access to scientific medical literature.

Installation

Prerequisites

Before installing, you'll need:

• Python installed on your system
• An email address to provide to NCBI (required)
• Optionally, an NCBI API key for higher rate limits

Installation Methods

Option 1: Install via Smithery (Recommended for Claude Desktop)

npx -y @smithery/cli install mcp-simple-pubmed --client claude

Option 2: Install via pip

pip install mcp-simple-pubmed

Configuration

The server requires configuration with your email address and optionally an API key:

• PUBMED_EMAIL: Your email address (required by NCBI)
• PUBMED_API_KEY: Optional API key for higher rate limits

Without an API key, the standard rate limit is 3 requests per second. With an API key, this increases to 10 requests per second. You can register for an API key at the NCBI website.

Setup for Claude Desktop

Add the following to your Claude Desktop configuration file (claude_desktop_config.json):

For macOS:

{
  "mcpServers": {
    "simple-pubmed": {
      "command": "python",
      "args": ["-m", "mcp_simple_pubmed"],
      "env": {
        "PUBMED_EMAIL": "your-email@example.com",
        "PUBMED_API_KEY": "your-api-key"
      }
    }
  }
}

For Windows:

{
  "mcpServers": {
    "simple-pubmed": {
      "command": "C:\\Users\\YOUR_USERNAME\\AppData\\Local\\Programs\\Python\\Python311\\python.exe",
      "args": [
        "-m",
        "mcp_simple_pubmed"
      ],
      "env": {
        "PUBMED_EMAIL": "your-email@example.com",
        "PUBMED_API_KEY": "your-api-key"
      }
    }
  }
}

Usage Notes

• The tool returns XML-formatted full text, which provides AI assistants with additional structural information about the document.
• If full text is not available through this tool, it may be because:
  • The article is behind a paywall
  • The article is available but not directly through PubMed
  • Access restrictions are in place
• For articles not accessible through this tool, you may still be able to access them through:
  • A regular web browser
  • Institutional library access
  • Other research access services

Limitations

• Cannot access paywalled or subscription-only papers
• Depends on PubMed/NCBI API availability
• Subject to NCBI's rate limits and terms of service