About pubmed_search MCP server
pubmed_search is an MCP server for searching PubMed through MCP clients. The README describes a simple note storage system with resources, a prompt and a tool, and the search capability is only briefly stated.
Key features
- 01Searches PubMed through MCP
- 02note:// URI scheme for individual notes
- 03summarize-notes prompt with style option
- 04add-note tool that notifies clients of changes
Use cases
- 01Configuring a PubMed search server in Claude Desktop
- 02Debugging the server with MCP Inspector
MCP support
This is an MCP server that exposes note resources, the summarize-notes prompt and the add-note tool to MCP clients.
Configuration
Local server config is the same for every client. Copy it into your client’s MCP config file.
We haven’t collected a package or remote endpoint for this server. Follow the instructions in the project README.
Tools
Local servers expose tools only once running on your machine, and the maintainer has not provided a tool list.
Details
From the project READMEpubmed_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
Development/Unpublished Servers Configuration
``` "mcpServers": { "pubmed_search": { "command": "uv", "args": [ "--directory", "/Users/nofuture/Documents/GitHub/pubmed_search", "run", "pubmed_search" ] } } ```Published Servers Configuration
``` "mcpServers": { "pubmed_search": { "command": "uvx", "args": [ "pubmed_search" ] } } ```Development
Building and Publishing
To prepare the package for distribution:
- Sync dependencies and update lockfile:
uv sync
- Build package distributions:
uv build
This will create source and wheel distributions in the dist/ directory.
- Publish to PyPI:
uv publish
Note: You'll need to set PyPI credentials via environment variables or command flags:
- Token:
--tokenorUV_PUBLISH_TOKEN - Or username/password:
--username/UV_PUBLISH_USERNAMEand--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.
Comments
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