MCP Simple Pubmed

🚀 Simple PubMed MCP Server

A simple MCP server that provides access to PubMed articles via the Entrez API.

🚀 Quick Start

This is an MCP server that offers access to PubMed articles through the Entrez API.

✨ Features

• Search the PubMed database using keywords.
• Access article abstracts.
• Download full-text articles (when they are open access on PubMed).

Please note that the tool returns full-text articles in XML format. This is more useful for AI as it provides additional information about the document structure. At least, this is what Claude 3.5 Sonnet prefers.

Also, note that the fact that this tool and others may not provide the full text of a paper does not necessarily mean the paper is unavailable. During testing, I encountered a paper with no full text on PubMed, and Claude got a "Forbidden" error when accessing the publication URL via the DOI. However, I was able to access the same page using a regular browser.

In short, if your AI assistant fails to obtain the full text of a paper through this tool, try accessing it manually using a regular browser.

Finally, this tool, of course, cannot provide access to paid journal articles. You may need to access them through your library resources or— as a last resort— through a website aiming to make publicly funded research freely available.

📦 Installation

Install via Smithery

To automatically install Simple PubMed for Claude Desktop via Smithery:

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

Manual Installation

pip install mcp-simple-pubmed

📚 Documentation

Configuration

The server requires the following environment variables:

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

The standard rate is 3 requests per second. Rate limits are not enforced as it's unlikely that AI-generated traffic will exceed this limit under normal circumstances. If needed, you can register for an API key to get a rate of 10 requests per second. Read the relevant content on the NCBI page.

Usage with Claude Desktop

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

Mac OS

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

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" 
      }
    }
  }
}

📄 License

MIT License