CarlosIrineuCosta/pubmed-mcp-enhanced

PubMed MCP Server - Enhanced Research Edition

Advanced AI-powered biomedical research assistant with enhanced PubMed integration and intelligent article discovery.

Based on: PubMed-MCP-Server by JackKuo666
Enhanced by: CarlosIrineuCosta (https://github.com/CarlosIrineuCosta) with advanced research features and AI-assisted workflows

This enhanced PubMed MCP Server provides a comprehensive bridge between AI assistants and biomedical literature, featuring advanced search capabilities, related article discovery, and AI-powered research workflows through the Model Context Protocol (MCP).

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Core Features

• Paper Search: Query PubMed articles with keywords or advanced search
• Efficient Retrieval: Fast access to paper metadata
• Metadata Access: Retrieve detailed metadata for specific papers
• Research Support: Facilitate biomedical sciences research and analysis
• Paper Access: Attempt to download full-text PDF content
• Deep Analysis: Perform comprehensive analysis of papers
• Research Prompts: A set of specialized prompts for paper analysis

Quick Start

Prerequisites

• Python 3.10+
• FastMCP library

Installation

Installing via Smithery

To install pubmed-mcp-server for Claude Desktop automatically via Smithery:

claude

npx -y @smithery/cli install @JackKuo666/pubmed-mcp-server --client claude

Cursor

Paste the following into Settings → Cursor Settings → MCP → Add new server:

• Mac/Linux

npx -y @smithery/cli@latest run @JackKuo666/pubmed-mcp-server --client cursor --config "{}" 

Windsurf

npx -y @smithery/cli@latest install @JackKuo666/pubmed-mcp-server --client windsurf --config "{}"

CLine

npx -y @smithery/cli@latest install @JackKuo666/pubmed-mcp-server --client cline --config "{}"

1. Clone the repository:

   git clone https://github.com/JackKuo666/PubMed-MCP-Server.git
   cd PubMed-MCP-Server
   

2. Install the required dependencies:

   pip install -r requirements.txt
   

Usage

Start the MCP server:

python pubmed_server.py

Usage with Claude Desktop

Add this configuration to your claude_desktop_config.json:

(Mac OS)

{
  "mcpServers": {
    "pubmed": {
      "command": "python",
      "args": ["-m", "pubmed-mcp-server"]
      }
  }
}

(Windows version):

{
  "mcpServers": {
    "pubmed": {
      "command": "C:\\Users\\YOUR\\PATH\\miniconda3\\envs\\mcp_server\\python.exe",
      "args": [
        "D:\\code\\YOUR\\PATH\\PubMed-MCP-Server\\pubmed_server.py"
      ],
      "env": {},
      "disabled": false,
      "autoApprove": []
    }
  }
}

Using with Cline

{
  "mcpServers": {
    "pubmed": {
      "command": "bash",
      "args": [
        "-c",
        "source /home/YOUR/PATH/mcp-server-pubmed/.venv/bin/activate && python /home/YOUR/PATH/pubmed-mcp-server.py"
      ],
      "env": {},
      "disabled": false,
      "autoApprove": []
    }
  }
}

MCP Tools

The PubMed MCP Server provides the following tools:

1. search_pubmed_key_words: Search for articles on PubMed using keywords.
2. search_pubmed_advanced: Perform an advanced search for articles on PubMed with multiple parameters.
3. get_pubmed_article_metadata: Fetch metadata for a PubMed article using its PMID.
4. download_pubmed_pdf: Attempt to download the full-text PDF for a PubMed article.
5. deep_paper_analysis: Perform a comprehensive analysis of a PubMed article.

Searching Papers

You can ask the AI assistant to search for papers using queries like:

Can you search PubMed for recent papers about CRISPR?

Getting Paper Details

Once you have a PMID, you can ask for more details:

Can you show me the metadata for the paper with PMID 12345678?

Analyzing Papers

You can request a deep analysis of a paper:

Can you perform a deep analysis of the paper with PMID 12345678?

Project Structure

• pubmed_server.py: The main MCP server implementation using FastMCP
• pubmed_web_search.py: Contains the logic for searching PubMed and retrieving article information

Dependencies

• Python 3.10+
• FastMCP
• asyncio
• logging
• requests
• beautifulsoup4

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

License

This project is licensed under the MIT License.

Disclaimer

This tool is for research purposes only. Please respect PubMed's terms of service and use this tool responsibly.