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 v0.5.13

• 🔧 NCBI Email 自動偵測: 不再需要手動設定 email，自動讀取 git config user.email
• 🛡️ EPERM 修復: 重新安裝時自動終止佔用的 Python 程序，避免 EPERM: unlink python.exe 錯誤
• 🐍 Python 3.12: 環境升級至 Python 3.12，更好的效能和語法支持
• 📦 PubMed Search MCP v0.3.8: 統一搜尋入口 unified_search，支援預印本、同行審查篩選

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 (v0.3.8)

• unified_search - 統一搜尋入口，自動合併去重多來源結果
• Multi-source search (PubMed, Europe PMC, CORE)
• 預印本搜尋 - 支援 arXiv、medRxiv、bioRxiv（include_preprints）
• 同行審查篩選 - 只顯示同行審查文章（peer_reviewed_only）
• Parse PICO clinical questions
• Find related and citing articles
• Get citation metrics (RCR)
• ICD ↔ MeSH 轉換 - 自動轉換 ICD 代碼和 MeSH 術語
• 研究時間軸 - 建構與比較研究領域的歷史演進
• 生物醫學圖片搜尋 - 搜尋 Open-i 和 Europe PMC 圖片
• Full-text access (Europe PMC, CORE)
• Session management (retrieve previous search results)
• NCBI 延伸 (Gene, PubChem, ClinVar)
• Export in multiple formats (RIS, BibTeX, etc.)

🌐 Connected APIs

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 3.12 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:

1. Search → Review → Ask Collection → Import workflow
2. Use get_session_pmids instead of re-searching
3. Use cached articles to save API quota
4. Check for duplicates before importing

Run Zotero MCP: Install Copilot Research Skills to manually install/update.

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 3.12
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
5. Copilot Skills: Installs research workflow guides to workspace

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

Copilot not using tools correctly

1. Run Zotero MCP: Install Copilot Research Skills to update workflow guides
2. The guides teach Copilot the correct order of operations

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.