PubMed
An MCP server that provides access to PubMed articles through the Entrez API.
What is PubMed?
PubMed is a Model Context Protocol (MCP) server that allows AI assistants like Claude, Cursor, and VS Code to mcp server that provides access to pubmed articles through the entrez api.
An MCP server that provides access to PubMed articles through the Entrez API.
This server falls under the Search & Data Extraction category on MCPgee, the world's largest MCP server directory with 33,000+ servers.
Features
- An MCP server that provides access to PubMed articles throug
Use Cases
Maintainer
Works with
Installation
NPM
npx -y mcp-simple-pubmedManual Installation
npx -y mcp-simple-pubmedConfiguration
Configuration Details
claude_desktop_config.json
Performance
Response Metrics
Resource Usage
How to Set Up and Use PubMed
MCP Simple PubMed gives AI assistants direct access to the PubMed biomedical literature database via the NCBI Entrez API, supporting keyword searches, MeSH term queries, Boolean operators, author lookups, and full-text retrieval for open-access PubMed Central articles. Researchers, clinicians, and developers use it to pull peer-reviewed evidence into Claude conversations — searching millions of life-science papers without leaving their AI workflow. It also includes guided prompts for systematic reviews, PICO clinical question searches, and author publication searches.
Prerequisites
- Python 3.10 or higher installed
- pip or uvx available for package installation
- An NCBI account email address (required by the Entrez API terms of service)
- An NCBI API key (optional but recommended for higher rate limits — 10 req/sec vs 3 req/sec)
- An MCP client such as Claude Desktop
Install the mcp-simple-pubmed package
Install the package from PyPI using pip. It will be available as the mcp_simple_pubmed Python module.
pip install mcp-simple-pubmedObtain an NCBI API key (recommended)
Register at NCBI (https://www.ncbi.nlm.nih.gov/account/) and generate an API key from your account settings. This raises your rate limit from 3 to 10 requests per second.
Configure Claude Desktop
Add the server to your claude_desktop_config.json. PUBMED_EMAIL is required by NCBI; PUBMED_API_KEY is optional but strongly recommended.
{
"mcpServers": {
"simple-pubmed": {
"command": "python",
"args": ["-m", "mcp_simple_pubmed"],
"env": {
"PUBMED_EMAIL": "[email protected]",
"PUBMED_API_KEY": "your_ncbi_api_key"
}
}
}
}Restart Claude Desktop
Restart the Claude Desktop application so it picks up the new server configuration. You should see PubMed search tools appear in the available tools list.
Run your first PubMed search
Ask Claude to search PubMed for a topic. The server supports keyword searches, MeSH terms, author names, date ranges, and Boolean AND/OR/NOT operators.
PubMed Examples
Client configuration
Claude Desktop configuration for mcp-simple-pubmed using the installed Python module.
{
"mcpServers": {
"simple-pubmed": {
"command": "python",
"args": ["-m", "mcp_simple_pubmed"],
"env": {
"PUBMED_EMAIL": "[email protected]",
"PUBMED_API_KEY": "your_ncbi_api_key"
}
}
}
}Prompts to try
Example research prompts to use once mcp-simple-pubmed is connected to Claude Desktop.
- "Search PubMed for randomized controlled trials on metformin and cardiovascular outcomes published after 2020"
- "Find papers by author 'Smith JA' on CRISPR gene editing"
- "Search PubMed for (diabetes[MeSH] AND insulin resistance) NOT type 1, limit to last 3 years"
- "Generate a systematic review search strategy for the PICO question: In adults with hypertension, does a low-sodium diet reduce cardiovascular events compared to normal diet?"
- "Get the full text of PMID 37234567 if it is open access"
- "Find the 10 most recent papers on mRNA vaccine efficacy"Troubleshooting PubMed
Rate limit errors (HTTP 429) when searching PubMed
Without an API key, NCBI allows only 3 requests per second. Register for a free NCBI API key at https://www.ncbi.nlm.nih.gov/account/ and add it as PUBMED_API_KEY in your config to raise the limit to 10 requests per second.
Module not found error: 'mcp_simple_pubmed'
Ensure you installed the package with 'pip install mcp-simple-pubmed' (note the hyphen) and that Claude Desktop is using the same Python interpreter. If using a virtual environment, use the full path to the Python executable in the 'command' field of your config.
Full text retrieval returns no content for an article
Full text is only available for open-access articles archived in PubMed Central (PMC). If an article is behind a paywall, only the abstract and metadata will be returned. Check if the article has a PMC ID (PMCID) for guaranteed full text access.
Frequently Asked Questions about PubMed
What is PubMed?
PubMed is a Model Context Protocol (MCP) server that mcp server that provides access to pubmed articles through the entrez api. It connects AI assistants to external tools and data sources through a standardized interface.
How do I install PubMed?
Install via npm with the command: npx -y mcp-simple-pubmed. Then add the server configuration to your AI client's JSON config file (e.g., claude_desktop_config.json or .cursor/mcp.json).
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.
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