This repository contains an MCP server that searches PubMed for article abstracts using BioPython's Entrez module. It leverages the FastMCP framework to provide asynchronous search capabilities for PubMed.

• Search PubMed: Query for articles based on a search term.
• Retrieve Abstracts: Fetch abstracts of articles returned from PubMed.
• Asynchronous Operation: Uses asynchronous execution (via asyncio.to_thread) to avoid blocking the server.

• Python 3.8 or higher
• mcp[cli]
• BioPython

1. Clone the Repository:

   git clone PubMed-MCP-Server.git
   cd PubMed-MCP-Server

2. Install Dependencies:

   You can install the required packages using uv:

   uv add -r requirements.txt

3. Configure Entrez Email:

   Ensure you have set a valid email address in the code (in main.py):

   Entrez.email = "give an email address"

Start the PubMed MCP server by running:

uv run main.py

This command starts the server using the uv command-line tool (as specified in your configuration).

To configure your MCP client to connect to the PubMed MCP server, create or update your config.json file as follows:

{
  "mcpServers": {
    "pubmed": {
      "command": "C:/Users/codingaslu/.local/bin/uv",
      "args": [
        "--directory",
        "C:/Users/codingaslu/OneDrive/Desktop/pubmed-mcp-server",
        "run",
        "main.py"
      ]
    }
  }
}

• command:
  The full path to the command-line tool used to run the MCP server (in this case, uv).

• args:

  • --directory: Specifies the working directory where the server is located.
  • "C:/Users/aiany/OneDrive/Desktop/YT Video/pubmed-mcp-server": The path to the server's root directory.
  • "run" and "main.py": The command and entry point to start the PubMed MCP server.

Once the server is running and your MCP client is configured, you can use the provided tool:

• Tool: search_pubmed
• Parameters:
  • query: The search term for PubMed (default is "endocarditis").
  • max_results: Maximum number of articles to retrieve (default is 10).

Example Usage:

search_pubmed(query="endocarditis", max_results=10)

This will return a string with the abstracts of the articles separated by newlines.

This project is licensed under the MIT License.

You can adjust paths and details as needed for your specific setup.