MCP PubMed Search

GitHub
  • Research & Data
Python
MIT
1
  • Apple
A
security – no known vulnerabilities (report Issue)
A
license - permissive license (MIT)
A
quality - confirmed to work

Server to search PubMed (PubMed is a free, online database that allows users to search for biomedical and life sciences literature). I have created on a day MCP came out but was on vacation, I saw someone post similar server in your DB, but figured to post mine.

  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
ENTREZ_EMAILYes
Need Help?View Source CodeReport Issue
README.md

pubmed_search MCP server

search pubmed via MCP

Components

Resources

The server implements a simple note storage system with:

  • Custom note:// URI scheme for accessing individual notes
  • Each note resource has a name, description and text/plain mimetype

Prompts

The server provides a single prompt:

  • summarize-notes: Creates summaries of all stored notes
    • Optional "style" argument to control detail level (brief/detailed)
    • Generates prompt combining all current notes with style preference

Tools

The server implements one tool:

  • add-note: Adds a new note to the server
    • Takes "name" and "content" as required string arguments
    • Updates server state and notifies clients of resource changes

Configuration

[TODO: Add configuration details specific to your implementation]

Quickstart

Install

Claude Desktop

On MacOS: ~/Library/Application\ Support/Claude/claude_desktop_config.json On Windows: %APPDATA%/Claude/claude_desktop_config.json

<details> <summary>Development/Unpublished Servers Configuration</summary> ``` "mcpServers": { "pubmed_search": { "command": "uv", "args": [ "--directory", "/Users/nofuture/Documents/GitHub/pubmed_search", "run", "pubmed_search" ] } } ``` </details> <details> <summary>Published Servers Configuration</summary> ``` "mcpServers": { "pubmed_search": { "command": "uvx", "args": [ "pubmed_search" ] } } ``` </details>

Development

Building and Publishing

To prepare the package for distribution:

  1. Sync dependencies and update lockfile:
uv sync
  1. Build package distributions:
uv build

This will create source and wheel distributions in the dist/ directory.

  1. Publish to PyPI:
uv publish

Note: You'll need to set PyPI credentials via environment variables or command flags:

  • Token: --token or UV_PUBLISH_TOKEN
  • Or username/password: --username/UV_PUBLISH_USERNAME and --password/UV_PUBLISH_PASSWORD

Debugging

Since MCP servers run over stdio, debugging can be challenging. For the best debugging experience, we strongly recommend using the MCP Inspector.

You can launch the MCP Inspector via npm with this command:

npx @modelcontextprotocol/inspector uv --directory /Users/nofuture/Documents/GitHub/pubmed_search run pubmed-search

Upon launching, the Inspector will display a URL that you can access in your browser to begin debugging.

GitHub Badge

Glama performs regular codebase and documentation scans to:

  • Confirm that the MCP server is working as expected.
  • Confirm that there are no obvious security issues with dependencies of the server.
  • Extract server characteristics such as tools, resources, prompts, and required parameters.

Our directory badge helps users to quickly asses that the MCP server is safe, server capabilities, and instructions for installing the server.

Copy the following code to your README.md file:

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