Zotero + PubMed MCP Extension for VS Code

🔬 AI-powered research assistant - Integrates Zotero reference management and PubMed literature search with GitHub Copilot.

Features

This extension provides two MCP (Model Context Protocol) servers that enable AI assistants like GitHub Copilot to:

📚 Zotero Keeper

• Search and browse your Zotero library
• Add references from PubMed or DOI
• Manage collections and tags
• Smart duplicate detection
• Batch import from PubMed searches

🔍 PubMed Search

• Search PubMed literature with MeSH terms
• Parse PICO clinical questions
• Find related and citing articles
• Get citation metrics (RCR)
• Export in multiple formats (RIS, BibTeX, etc.)

Requirements

• VS Code 1.99.0 or later
• Zotero 7 running locally (for Zotero features)

Note: Python is managed automatically by the extension using uv.

Installation

1. Install this extension from the VS Code Marketplace
2. The extension will automatically:
   • Download uv (fast Python package manager, ~10MB)
   • Create an isolated Python 3.11 environment
   • Install required packages (zotero-keeper, pubmed-search-mcp)
   • Register MCP servers with VS Code

Usage

Once installed, the MCP tools will be available to GitHub Copilot. Try asking:

• "Search PubMed for remimazolam sedation"
• "Find recent articles about CRISPR gene editing"
• "Save this article to my Zotero library"
• "Show my recent Zotero references"

Extension Settings

Commands

How It Works

This extension uses uv from Astral to manage Python:

1. First Run: Downloads uv binary (~10MB) to extension storage
2. Environment Setup: Creates isolated venv with Python 3.11
3. Package Install: Installs zotero-keeper and pubmed-search-mcp (10-100x faster than pip)
4. MCP Servers: Starts both servers and registers with VS Code

The Python environment is completely isolated from your system Python.

Troubleshooting

Cannot connect to Zotero

1. Make sure Zotero 7 is running
2. Check that the API is enabled (Edit → Settings → Advanced → Allow other applications...)
3. Verify host/port settings match your setup

Extension not activating

1. Check the "Zotero MCP" output channel for errors
2. Try running Zotero MCP: Reinstall Python Environment command
3. Restart VS Code

uv download failed

1. Check your internet connection
2. Check if your firewall blocks downloads from github.com
3. The extension will retry on next activation

Related Projects

• zotero-keeper - Zotero MCP server
• pubmed-search-mcp - PubMed MCP server
• uv - Fast Python package manager
• Model Context Protocol - MCP specification

License

Apache-2.0

Contributing

Contributions welcome! Please see CONTRIBUTING.md.