Zotero + PubMed MCP Extension for VS Code
🔬 AI-powered research assistant - Integrates Zotero reference management and PubMed literature search with GitHub Copilot.
✨ What's New in v0.5.2
- 📊 Usage Statistics: Track searches, imports, and full-text accesses
- 🌐 API Status Dashboard: View and manage 8 connected APIs at a glance
- 📋 Quick Menu: Click status bar for instant access to all features
- 🔢 Version Display: Status bar shows current version
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
- Library analytics (stats, orphan detection)
🔍 PubMed Search
- Search PubMed literature with MeSH terms
- Multi-source search (Europe PMC, CORE, Semantic Scholar)
- Parse PICO clinical questions
- Find related and citing articles
- Get citation metrics (RCR)
- Full-text access (Europe PMC, CORE)
- Session management (retrieve previous search results)
- Export in multiple formats (RIS, BibTeX, etc.)
🌐 Connected APIs
| API |
Description |
| PubMed / NCBI |
36M+ biomedical articles |
| Europe PMC |
33M+ articles, full-text, text mining |
| CORE |
200M+ open access papers |
| Semantic Scholar |
AI-powered recommendations |
| PubChem |
Chemical compound database |
| NCBI Gene |
Gene information |
| ClinVar |
Clinical variants |
| Zotero Local |
Reference management |
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
- Install this extension from the VS Code Marketplace
- 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
- Install Copilot research workflow guides
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"
- "Get my last search results" (uses session management)
📊 Status Bar
Click the status bar item to access:
- 📊 Usage Statistics - Track your research activity
- 🌐 API Status - View/configure connected APIs
- ⚙️ Settings - Quick access to configuration
- 🧙 Setup Wizard - One-click setup
🎯 Copilot Research Skills
The extension installs workflow guides that teach Copilot:
- Search → Review → Ask Collection → Import workflow
- Use
get_session_pmids instead of re-searching
- Use cached articles to save API quota
- Check for duplicates before importing
Run Zotero MCP: Install Copilot Research Skills to manually install/update.
Extension Settings
| Setting |
Default |
Description |
zoteroMcp.zoteroHost |
localhost |
Zotero host address |
zoteroMcp.zoteroPort |
23119 |
Zotero API port |
zoteroMcp.ncbiEmail |
|
Email for NCBI API (recommended) |
zoteroMcp.enableZoteroKeeper |
true |
Enable Zotero Keeper server |
zoteroMcp.enablePubmedSearch |
true |
Enable PubMed Search server |
Commands
| Command |
Description |
Zotero MCP: Setup Wizard |
One-click setup |
Zotero MCP: Quick Menu |
Show quick access menu |
Zotero MCP: Show Statistics |
View usage statistics |
Zotero MCP: Show API Status |
View connected APIs |
Zotero MCP: Check Zotero Connection |
Verify Zotero is accessible |
Zotero MCP: Install Copilot Research Skills |
Install workflow guides |
Zotero MCP: Reinstall Python Environment |
Reinstall uv and Python packages |
Zotero MCP: Show Status |
Show full extension status |
Zotero MCP: Open Settings |
Open extension settings |
How It Works
This extension uses uv from Astral to manage Python:
- First Run: Downloads uv binary (~10MB) to extension storage
- Environment Setup: Creates isolated venv with Python 3.11
- Package Install: Installs
zotero-keeper and pubmed-search-mcp (10-100x faster than pip)
- MCP Servers: Starts both servers and registers with VS Code
- Copilot Skills: Installs research workflow guides to workspace
The Python environment is completely isolated from your system Python.
Troubleshooting
Cannot connect to Zotero
- Make sure Zotero 7 is running
- Check that the API is enabled (Edit → Settings → Advanced → Allow other applications...)
- Verify host/port settings match your setup
Extension not activating
- Check the "Zotero MCP" output channel for errors
- Try running
Zotero MCP: Reinstall Python Environment command
- Restart VS Code
- Run
Zotero MCP: Install Copilot Research Skills to update workflow guides
- The guides teach Copilot the correct order of operations
uv download failed
- Check your internet connection
- Check if your firewall blocks downloads from
github.com
- The extension will retry on next activation
License
Apache-2.0
Contributing
Contributions welcome! Please see CONTRIBUTING.md.
