mcp-simple-pubmed

GitHub
  • Research & Data
Python
MIT
  • Apple
A
security – no known vulnerabilities (report Issue)
A
license - permissive license (MIT)
A
quality - confirmed to work

An MCP server that provides access to PubMed articles through the Entrez API.

  1. Tools
  2. Prompts
  3. Resources
  4. Server Configuration
  5. README.md

Prompts

Interactive templates invoked by user choice

NameDescription

No prompts

Resources

Contextual data attached and managed by the client

NameDescription

No resources

Tools

Functions exposed to the LLM to take actions

NameDescription

No tools

Server Configuration

Describes the environment variables required to run the server.

NameRequiredDescriptionDefault
PUBMED_EMAILYes
PUBMED_API_KEYNoAPI key for higher rate limits
Need Help?View Source CodeReport Issue
README.md

MCP Simple PubMed

An MCP server that provides access to PubMed articles through the Entrez API.

<a href="https://glama.ai/mcp/servers/5wlfb8i6bj"><img width="380" height="200" src="https://glama.ai/mcp/servers/5wlfb8i6bj/badge" alt="mcp-simple-pubmed MCP server" /></a>

Features

  • Search PubMed database using keywords
  • Access article abstracts
  • Download full text when available (for open access articles available directly on PubMed)

Please note that the tool returns XML-ized version of full text. It is however more useful for AIs than a "human readable" text would have been as it gives them additional information about document's structure. At least, this is what Claude 3.5 Sonnet said he prefers.

Please also note that inability of this tool and possibly other tools to deliver a paper's full text may not be due to the fact that it is not available. When testing this tool I came across a paper that did not have full text on PubMed and when Claude accessed the publication URL (which we did get through DOI) using fetch he did get a "forbidden” error. However, I was able to access the very same page using a regular browser.

In other words if your AI assistant is not able to get the full text of a paper using this tool it is worth trying manually with a regular web browser.

Finally, this tool of course can’t give you access to paywalled/paid papers. You may be able to read them through your library access or – as a last resort – through a certain site that strives to make publicly funded research freely available.

Installation

pip install mcp-simple-pubmed

Configuration

The server requires the following environment variables:

  • PUBMED_EMAIL: Your email address (required by NCBI)
  • PUBMED_API_KEY: Optional API key for higher rate limits

The standard rate limit is 3 requests / second. No rate limiting was implemented, as it is highly unlikely in the typical usage scenario that your AI would generate more traffic. If you need it, you can register for an API key which will give you 10 requests / second. Read about this on NCBI pages.

Usage with Claude Desktop

Add to your Claude Desktop configuration (claude_desktop_config.json):

(Mac OS)

{ "mcpServers": { "simple-pubmed": { "command": "python", "args": ["-m", "mcp_simple_pubmed"], "env": { "PUBMED_EMAIL": "your-email@example.com", "PUBMED_API_KEY": "your-api-key" } } } }

(Windows)

{ "mcpServers": { "simple-pubmed": { "command": "C:\\Users\\YOUR_USERNAME\\AppData\\Local\\Programs\\Python\\Python311\\python.exe", "args": [ "-m", "mcp_simple_pubmed" ], "env": { "PUBMED_EMAIL": "your-email@example.com", "PUBMED_API_KEY": "your-api-key" } } } }

License

MIT License

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