PubMed
Provides comprehensive access to NCBI's PubMed database of over 36 million biomedical citations, allowing users to search, retrieve, and analyze literature directly through MCP tools. It supports advanced queries, citation management, full-text retri
What is PubMed?
PubMed is a Model Context Protocol (MCP) server that allows AI assistants like Claude, Cursor, and VS Code to provides comprehensive access to ncbi's pubmed database of over 36 million biomedical citations, allowing users to search, retrieve, and analyze literature directly through mcp tools. it supports adva...
Provides comprehensive access to NCBI's PubMed database of over 36 million biomedical citations, allowing users to search, retrieve, and analyze literature directly through MCP tools. It supports advanced queries, citation management, full-text retri
This server falls under the Search & Data Extraction category on MCPgee, the world's largest MCP server directory with 33,000+ servers.
Features
- Provides comprehensive access to NCBI's PubMed database of o
Use Cases
Maintainer
Works with
Installation
Manual Installation
npx pubmed-mcp-serverConfiguration
Configuration Details
claude_desktop_config.json
Performance
Response Metrics
Resource Usage
How to Set Up and Use PubMed
PubMed MCP Server connects AI assistants to NCBI's PubMed database, which indexes over 36 million biomedical citations. It exposes tools for keyword search, advanced filtered queries, article metadata retrieval by PMID, PDF download attempts, and deep paper analysis — making it ideal for researchers, clinicians, and students who want to explore scientific literature without leaving their AI workflow.
Prerequisites
- Python 3.8 or higher installed
- pip and virtualenv for dependency management
- An MCP-compatible client such as Claude Desktop or Cline
- Git to clone the repository (or install via Smithery CLI)
Clone the repository
Clone the PubMed MCP Server repository from GitHub and navigate into it.
git clone https://github.com/JackKuo666/PubMed-MCP-Server.git
cd PubMed-MCP-ServerInstall Python dependencies
Install all required Python packages listed in requirements.txt.
pip install -r requirements.txtStart the server
Launch the PubMed MCP server. It will listen on stdio for MCP client connections.
python pubmed_server.pyAlternative: install via Smithery
You can also install directly via the Smithery CLI, which handles configuration automatically for Claude Desktop.
npx -y @smithery/cli install @JackKuo666/pubmed-mcp-server --client claudeAdd to Claude Desktop configuration
Edit your Claude Desktop config file (claude_desktop_config.json) to register the server. Replace the path with the actual path to pubmed_server.py on your system.
{
"mcpServers": {
"pubmed": {
"command": "python",
"args": ["/path/to/PubMed-MCP-Server/pubmed_server.py"]
}
}
}PubMed Examples
Client configuration
Claude Desktop configuration block for the PubMed MCP Server using a local Python installation.
{
"mcpServers": {
"pubmed": {
"command": "python",
"args": ["/path/to/PubMed-MCP-Server/pubmed_server.py"]
}
}
}Prompts to try
Example natural language prompts that exercise the five available tools: keyword search, advanced search, metadata lookup, PDF download, and deep analysis.
- "Search PubMed for recent papers about CRISPR gene editing published after 2022"
- "Find articles on COVID-19 mRNA vaccine efficacy with more than 500 citations"
- "Get the metadata for PubMed article PMID 35839922"
- "Perform a deep analysis of the paper with PMID 33446519"
- "Try to download the full-text PDF for PMID 34567890"Troubleshooting PubMed
Server fails to start with import errors
Ensure all dependencies are installed in the correct Python environment. Try running 'pip install -r requirements.txt' again, or use a virtual environment: 'python -m venv venv && source venv/bin/activate && pip install -r requirements.txt'.
PDF download returns 'no PDF available' for most articles
Full-text PDFs are only available for open-access articles. PubMed Central (PMC) hosts free full-text versions; for paywalled journals, only the abstract and metadata can be retrieved.
Claude Desktop does not show PubMed tools
Verify the config file path is correct for your OS (~/Library/Application Support/Claude/claude_desktop_config.json on macOS) and that the Python path in 'command' points to the correct interpreter. Restart Claude Desktop after saving the config.
Frequently Asked Questions about PubMed
What is PubMed?
PubMed is a Model Context Protocol (MCP) server that provides comprehensive access to ncbi's pubmed database of over 36 million biomedical citations, allowing users to search, retrieve, and analyze literature directly through mcp tools. it supports advanced queries, citation management, full-text retri It connects AI assistants to external tools and data sources through a standardized interface.
How do I install PubMed?
Follow the installation instructions on the PubMed GitHub repository. Clone the repo, install dependencies, and add the server config to your AI client.
Which AI clients work with PubMed?
PubMed works with all major MCP-compatible AI clients including Claude Desktop, Claude Code, Cursor, VS Code (GitHub Copilot), Windsurf, and Cline.
Is PubMed free to use?
Yes, PubMed is open source and available under the MIT License license. You can use it freely in both personal and commercial projects.
PubMed Alternatives — Similar Search & Data Extraction Servers
Looking for alternatives to PubMed? Here are other popular search & data extraction servers you can use with Claude, Cursor, and VS Code.
TrendRadar
★ 58.0kA real-time hotspot monitoring and news aggregation assistant that provides AI-powered analysis of trending topics across multiple platforms via the Model Context Protocol. It enables users to track news and receive automated notifications through va
Scrapling
★ 52.7k🕷️ An adaptive Web Scraping framework that handles everything from a single request to a full-scale crawl!
PDF Math Translate
★ 33.9k[EMNLP 2025 Demo] PDF scientific paper translation with preserved formats - 基于 AI 完整保留排版的 PDF 文档全文双语翻译，支持 Google/DeepL/Ollama/OpenAI 等服务，提供 CLI/GUI/MCP/Docker/Zotero
GPT Researcher
★ 27.2kAn autonomous agent that conducts deep research on any data using any LLM providers
Agent Reach
★ 20.1kGive your AI agent eyes to see the entire internet. Read & search Twitter, Reddit, YouTube, GitHub, Bilibili, XiaoHongShu — one CLI, zero API fees.
Xiaohongshu
★ 13.7kMCP for xiaohongshu.com
Browse More Search & Data Extraction MCP Servers
Explore all search & data extraction servers available in the MCPgee directory. Each server includes setup guides for Claude, Cursor, and VS Code.
Set Up PubMed in Your Editor
Choose your AI client for step-by-step setup instructions.
Quick Config Preview
Add this to your claude_desktop_config.json or .cursor/mcp.json
Ready to use PubMed?
Browse our complete directory of 33,000+ MCP servers, read setup guides for your editor, and start building with the Model Context Protocol.