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MCP PubMed Search

by wavelovey

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

Related MCP server: pubmed-search

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

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.

Available Tools

1 tool

TDQS

B3.1/5.0
Disambiguation5/5

With only one tool, there is no possibility of ambiguity or overlap between tools. The single tool's purpose is clearly defined as searching the PubMed database, leaving no room for misselection.

Naming Consistency5/5

A single tool inherently has perfect naming consistency, as there are no other tools to compare it against. The tool name 'pubmed_search' follows a clear verb_noun pattern that is appropriate for its function.

Tool Count2/5

One tool is too few for a server named 'MCP PubMed Search', which suggests a broader scope for interacting with PubMed. A single search tool feels thin and incomplete, lacking operations like filtering results, retrieving article details, or managing queries.

Completeness2/5

The tool surface is severely incomplete for a PubMed search domain. While searching is a core function, there are obvious gaps such as no ability to get article metadata, filter searches, save results, or handle citations, which limits agent workflows significantly.

Maintenance

ActivityInactive
ResponsivenessSyncing

Resources

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