NCBI PubMed
Provides seamless access to over 35 million PubMed scientific articles through natural language queries for research discovery and analysis. It enables tools for advanced searches, retrieving article details, and exploring related research within the
What is NCBI PubMed?
NCBI PubMed is a Model Context Protocol (MCP) server that allows AI assistants like Claude, Cursor, and VS Code to provides seamless access to over 35 million pubmed scientific articles through natural language queries for research discovery and analysis. it enables tools for advanced searches, retrieving article ...
Provides seamless access to over 35 million PubMed scientific articles through natural language queries for research discovery and analysis. It enables tools for advanced searches, retrieving article details, and exploring related research within the
This server falls under the Search & Data Extraction category on MCPgee, the world's largest MCP server directory with 33,000+ servers.
Features
- Provides seamless access to over 35 million PubMed scientifi
Use Cases
Maintainer
Works with
Installation
Manual Installation
npx ncbiConfiguration
Configuration Details
claude_desktop_config.json
Performance
Response Metrics
Resource Usage
How to Set Up and Use NCBI PubMed
The NCBI MCP Server provides AI assistants with direct access to over 35 million PubMed scientific articles through NCBI's Entrez API. It exposes tools for full-text search, article retrieval, MeSH term lookup, related article discovery, and advanced multi-criteria filtering — making it a powerful research companion for scientists, clinicians, and literature reviewers.
Prerequisites
- Python 3.8 or later installed
- Poetry package manager (recommended) or pip with venv
- An NCBI-registered email address (required by NCBI Entrez API policy)
- Optional: NCBI API key for higher rate limits (10 req/s vs 3 req/s) — free at ncbi.nlm.nih.gov/account/
- Claude Desktop or another MCP-compatible client
Clone and set up the project with Poetry
Clone the repository and install dependencies using Poetry.
git clone https://github.com/vitorpavinato/ncbi-mcp-server.git
cd ncbi-mcp-server
poetry installAlternative: set up with venv and pip
If you prefer pip over Poetry, create a virtual environment and install from requirements.txt.
python -m venv venv
source venv/bin/activate # On Windows: venv\Scripts\activate
pip install -r requirements.txtTest the server manually
Start the server to confirm it launches without errors. It communicates over stdio.
poetry run python src/ncbi_mcp_server/server.pyConfigure Claude Desktop
Add the NCBI server to your Claude Desktop config. Use the absolute path to the project directory. The server does not require environment variables but benefits from an NCBI API key passed via tool arguments.
Restart Claude Desktop and run a search
Quit and reopen Claude Desktop. Ask Claude to search PubMed to verify the connection. The NCBI API requires your email in the request — Claude will prompt for it if not pre-configured.
NCBI PubMed Examples
Client configuration
Claude Desktop config using Poetry to launch the NCBI MCP server.
{
"mcpServers": {
"ncbi-literature": {
"command": "poetry",
"args": ["run", "python", "src/ncbi_mcp_server/server.py"],
"cwd": "/absolute/path/to/ncbi-mcp-server"
}
}
}Prompts to try
Research queries that leverage the full PubMed search capabilities.
- "Search PubMed for 'CRISPR AND cancer[ti]' and summarize the top 5 results."
- "Get article details for PMIDs 38000001, 38000002, and 38000003."
- "Find MeSH terms related to 'Alzheimer disease' for use in a precise search."
- "Search for review articles in Nature or Science about machine learning in genomics from the last 2 years."
- "Find articles related to PMID 35000000 and identify common themes."Troubleshooting NCBI PubMed
NCBI API returns 429 Too Many Requests
Without an API key, NCBI limits requests to 3 per second. Obtain a free API key at ncbi.nlm.nih.gov/account/ to raise the limit to 10 per second. Pass the key to tool calls via the api_key parameter.
Poetry command not found when Claude Desktop tries to start the server
Use the full path to the Poetry executable in the config, e.g., "/home/user/.local/bin/poetry". Find the path with `which poetry`. Alternatively switch to the venv+pip setup and use `python` as the command.
Server fails with ImportError on startup
Ensure you ran `poetry install` (or `pip install -r requirements.txt`) from within the project directory. Check that the cwd in claude_desktop_config.json matches the absolute path to the cloned repository.
Frequently Asked Questions about NCBI PubMed
What is NCBI PubMed?
NCBI PubMed is a Model Context Protocol (MCP) server that provides seamless access to over 35 million pubmed scientific articles through natural language queries for research discovery and analysis. it enables tools for advanced searches, retrieving article details, and exploring related research within the It connects AI assistants to external tools and data sources through a standardized interface.
How do I install NCBI PubMed?
Follow the installation instructions on the NCBI PubMed GitHub repository. Clone the repo, install dependencies, and add the server config to your AI client.
Which AI clients work with NCBI PubMed?
NCBI PubMed works with all major MCP-compatible AI clients including Claude Desktop, Claude Code, Cursor, VS Code (GitHub Copilot), Windsurf, and Cline.
Is NCBI PubMed free to use?
Yes, NCBI PubMed is open source and available under the MIT license. You can use it freely in both personal and commercial projects.
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Quick Config Preview
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