Pubmed Searcher

🚀 PubMed Analysis MCP Server

A self - developed MCP server by a struggling medical student. It's a newly developed project with features still being improved. Your suggestions and improvements are highly welcome!

A professional MCP server for analyzing PubMed medical literature, which helps researchers quickly gain insights into medical research dynamics.

🚀 Quick Start

The PubMed Analysis MCP Server is designed to assist in in - depth analysis of medical literature. Below are the steps and examples to get you started.

Installation

# Install dependencies
pip install -r requirements.txt
# Or use uv
uv pip install -r requirements.txt

Configuration

Configure the mcp.json file. Here is an example for Windows:

// Add the following configuration in mcp.json (for Windows)
"PubMed": {
        "command": "cmd",
        "args": [
          "/c",
          "path/to/python.exe",
          "path/to/server.py"
        ]
    }
// For example, my mcp.json file looks like this
{
    "mcpServers": {
      "fetch":{
        "command": "cmd",
        "args": [
          "/c",
          "uvx",
          "mcp-server-fetch"
        ]
      },
      "PubMed": {
        "command": "cmd",
        "args": [
          "/c",
          "path/to/python.exe",
          "path/to/server.py"
        ]
      }
    }
}

Example of Calling

// For example, call the analyze_research_hotspots tool:
python script.py --tool analyze_research_hotspots --filename results.json --top_n 50

✨ Features

• Literature Retrieval: Supports PubMed advanced search syntax with date filtering and allows setting the date range and the number of results.
• Hotspot Analysis: Analyzes keyword frequencies to identify popular research areas and summarizes relevant literature.
• Trend Tracking: Tracks keyword changes over time to reveal evolving research trends.
• Publication Count: Analyzes publication volume changes with customizable time periods.
• Comprehensive Reports: Generates complete reports with customizable parameters.

📦 MCP Tools

1. search_pubmed

Search PubMed and save results.

• Key parameters:
  • email: Your email (required)
  • advanced_search: PubMed search query (required, same as advanced search syntax)
  • max_results: Maximum results (default: 1000)

2. list_result_files

List available result files.

3. analyze_research_hotspots

Analyze research hotspots.

• Key parameters:
  • filename: Result filename (required)
  • top_n: Number of keywords (default: 20)

4. analyze_research_trends

Analyze research trends.

5. analyze_publication_count

Analyze publication counts.

6. generate_comprehensive_analysis

Generate comprehensive analysis.

💻 Usage Examples

Basic Usage

The basic usage involves installing dependencies, configuring the mcp.json file, and then calling the relevant tools as shown in the "Quick Start" section.

Advanced Usage

You can customize the parameters according to your specific needs. For example, when using the analyze_research_hotspots tool, you can adjust the top_n parameter to analyze a different number of keywords.

📄 Notes

⚠️ Important Note

Please comply with NCBI's API usage policies when using this server.

⚠️ Important Note

Analysis results will be saved in the specified path, please ensure the path is valid.

⚠️ Important Note

This project is still under development and may have unstable situations.

💡 Usage Tip

Welcome to provide suggestions and improvements!