medRxiv MCP Server

🔍 Enable AI assistants to search and access medRxiv papers through a simple MCP interface.

The medRxiv MCP Server provides a bridge between AI assistants and medRxiv's preprint repository through the Model Context Protocol (MCP). It allows AI models to search for health sciences preprints and access their content in a programmatic way.

🤝 Contribute • 📝 Report Bug

✨ Core Features

• 🔎 Paper Search: Query medRxiv papers with custom search strings ✅
• 🚀 Efficient Retrieval: Fast access to paper metadata ✅
• 📄 Paper Access: Download and read paper content 📝
• 📋 Paper Listing: View all downloaded papers 📝
• 🗃️ Local Storage: Papers are saved locally for faster access 📝
• 📝 Research Prompts: A set of specialized prompts for paper analysis 📝
• 📊 Research Support: Facilitate health sciences research and analysis 📝

🚀 Quick Start

Installing via Smithery

To install medRxiv Server for Claude Desktop automatically via Smithery:

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

Installing Manually

Install using uv:

uv tool install medRxiv-mcp-server

For development:

# Clone and set up development environment
git clone https://github.com/JackKuo666/medRxiv-MCP-Server.git
cd medRxiv-MCP-Server

# Create and activate virtual environment
uv venv
source .venv/bin/activate
uv pip install -r requirements.txt

📊 Usage

Start the MCP server:

python medrxiv_server.py

🛠 MCP Tools

Usage with Claude Desktop

Add this configuration to your claude_desktop_config.json:

(Mac OS)

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

(Windows version):

{
  "mcpServers": {
    "biorxiv": {
      "command": "C:\\Users\\YOUR_USERNAME\\AppData\\Local\\Programs\\Python\\Python311\\python.exe",
      "args": [
        "-m",
        "medrxiv-mcp-server"
      ]
    }
  }
}

Using with Cline

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

After restarting Claude Desktop, the following capabilities will be available:

Searching Papers

You can ask Claude to search for papers using queries like:

Can you search bioRxiv for recent papers about genomics?

The search will return basic information about matching papers including:

• Paper title

• Authors

• DOI

Getting Paper Details

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

Can you show me the details for paper 10.1101/003541?

This will return:

• Full paper title

• Authors

• Publication date

• Paper abstract

• Links to available formats (PDF/HTML)

📝 TODO

download_paper

Download a paper and save it locally.

read_paper

Read the content of a downloaded paper.

list_papers

List all downloaded papers.

📝 Research Prompts

The server offers specialized prompts to help analyze academic papers:

Paper Analysis Prompt

A comprehensive workflow for analyzing academic papers that only requires a paper ID:

result = await call_prompt("deep-paper-analysis", {
    "paper_id": "2401.12345"
})

This prompt includes:

• Detailed instructions for using available tools (list_papers, download_paper, read_paper, search_papers)
• A systematic workflow for paper analysis
• Comprehensive analysis structure covering:
  • Executive summary
  • Research context
  • Methodology analysis
  • Results evaluation
  • Practical and theoretical implications
  • Future research directions
  • Broader impacts

📁 Project Structure

• medrxiv_server.py: The main MCP server implementation using FastMCP
• medrxiv_web_search.py: Contains the web scraping logic for searching medRxiv

🔧 Dependencies

• Python 3.10+
• mcp[cli]>=1.4.1
• requests>=2.25.1
• beautifulsoup4>=4.9.3

🤝 Contributing

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

📄 License

This project is licensed under the MIT License.

🙏 Acknowledgements

This project is inspired by and built upon the work done in the arxiv-mcp-server project.

⚠️ Disclaimer

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