MCP 服务器

PubMed MCP Server

Enables AI assistants to search, access, and analyze PubMed articles through MCP, providing tools for keyword and advanced search, article metadata retrieval, full-text PDF download, and deep paper analysis.

README

PubMed MCP Server

🔍 Enable AI assistants to search, access, and analyze PubMed articles through a simple MCP interface.

The PubMed MCP Server provides a bridge between AI assistants and PubMed's vast repository of biomedical literature through the Model Context Protocol (MCP). It allows AI models to search for scientific articles, access their metadata, and perform deep analysis in a programmatic way.

🤝 Contribute • 📝 Report Bug

✨ 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 "{}"

Clone the repository:

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

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:

search_pubmed_key_words: Search for articles on PubMed using keywords.
search_pubmed_advanced: Perform an advanced search for articles on PubMed with multiple parameters.
get_pubmed_article_metadata: Fetch metadata for a PubMed article using its PMID.
download_pubmed_pdf: Attempt to download the full-text PDF for a PubMed article.
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