PubMed

by jackkuo666

64 stars

181 downloads

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GitHub

About

Provides a bridge to PubMed for searching, filtering, retrieving, and analyzing medical research articles with tools for keyword searches, metadata access, PDF downloads, and structured paper analysis.

Details

Author: jackkuo666
Repository: JackKuo666/PubMed-MCP-Server
GitHub stars: 64
Downloads: 181
License: MIT License
Categories: AI, Design, Developer Tools, Search, Infrastructure, Frontend, Security, Other, Knowledge Base
Tags: #integration

- 🔎 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 ✅

Setting up with Highlight

This MCP is not yet compatible with Highlight’s one-click setup. However, you can still use it with Highlight by following these steps:

Download and install Highlight from highlightai.com/download
Navigate to the plugins tab and select "Add Custom Plugin"
Configure the plugin with the settings below
Plugin Name PubMed

Command (node, npx, python, etc.) python
Arguments
- Argument 1 -m
- Argument 2 pubmed-mcp-server
Please refer to the README for specific instructions on how to obtain API keys or other required environment variables.
Enable "Start Automatically" if you want the plugin to start when Highlight launches

Setting up with Cursor

Open Cursor's settings
Navigate to the MCP section
Click "Add new Global MCP server"
Copy and paste the configuration below based on your operating system

JSON

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

JSON

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

JSON

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

Setting up with Claude Desktop

Open Claude Desktop's settings
Go to the Integrations tab
Click "Add MCP Server"
Use the configuration below based on your operating system

Note: Make sure Claude Desktop is running before attempting to connect.

JSON

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

JSON

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

JSON

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

Setting up with Windsurf

Open Windsurf's preferences
Go to the Integrations section
Click "Add MCP Integration"
Use the configuration below based on your operating system

JSON

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

JSON

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

JSON

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

Setting up with Cline

Open Cline's settings
Navigate to the Integrations section
Click "Add MCP Server"
Copy and paste the configuration below based on your operating system

Note: Make sure to restart Cline after adding the configuration.

JSON

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

JSON

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

JSON

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

Setting up with Goose

Open Goose's preferences
Go to the Integrations tab
Select "MCP Servers"
Click "Add New Server"
Use the configuration below based on your operating system

JSON

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

JSON

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

JSON

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

From the repository

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

Start the MCP server:

python pubmed_server.py

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": []
    }
  }
}

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

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

`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.

Claude Desktop / Cursor

Paste into your MCP client config file to install this server.

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

Linux

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

Macos

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

Windows

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

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 "{}"

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.

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About

Details

Jump to

Setting up with Highlight

From the repository

search_pubmed_key_words

search_pubmed_advanced

get_pubmed_article_metadata

download_pubmed_pdf

deep_paper_analysis

Claude Desktop / Cursor

Linux

Macos

Windows

PubMed MCP Server

✨ Core Features

🚀 Quick Start

Prerequisites

Installation

Installing via Smithery

claude

Cursor

Windsurf

CLine

📊 Usage

Usage with Claude Desktop

🛠 MCP Tools

Searching Papers

Getting Paper Details

Analyzing Papers

📁 Project Structure

🔧 Dependencies

🤝 Contributing

📄 License

⚠️ Disclaimer

Install

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`search_pubmed_key_words`

`search_pubmed_advanced`

`get_pubmed_article_metadata`

`download_pubmed_pdf`

`deep_paper_analysis`