Zotero + PubMed MCP Extension for VS Code

What's New in v0.5.30

• Release install stability: pins the extension-managed Zotero Keeper install to the new v0.5.30-ext archive so users receive the latest runtime fixes.
• PubMed citation metrics compatibility: accepts both sync and async PubMed Search MCP citation-metrics implementations.
• CI and VSIX asset checks: fixes cross-directory Cline skill audits and Windows-safe asset synchronization checks.

What's New in v0.5.29

• Codex MCP auto-configuration: extension now writes [mcp_servers.zotero-keeper] and [mcp_servers.pubmed-search-mcp] into Codex CLI's ~/.codex/config.toml automatically (parity with Cline). Honors $CODEX_HOME; preserves all unrelated user content.
• Cline auto-configuration now actually triggers: added onStartupFinished activation event so Cline-only sessions reliably populate cline_mcp_settings.json instead of staying empty.

What's New in v0.5.28

• Windows-safe installs and upgrades: system/custom Python fallback now creates a writable extension-managed venv before uv pip install, avoiding protected paths such as C:\Python314\Lib\site-packages.
• Codex/Cline harness refresh: VSIX installs Codex AGENTS.md, .codex/skills, Cline MCP settings, and curated assistant skills while preserving user customizations.
• VSIX release guards: packaging, asset sync, version sync, and direct VSIX content checks now verify the shipped harness and package sources.

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

✨ What's New in v0.5.26

• PubMed Search 0.5.6 baseline: updates the bundled PubMed Search MCP snapshot to the latest upstream tag with Entrez runtime stability fixes.
• Cline asset compatibility: fixes strict YAML frontmatter for bundled skills and packages Zotero/PubMed Cline rules into the VSIX.
• Marketplace banner fix: uses a GitHub raw image URL so the VSIX details page renders the banner correctly.

✨ What's New in v0.5.25

• 🚀 Ready-to-publish maintenance: this release aligns VSIX metadata and installer source URL after the 0.5.24 hotfix.

✨ What's New in v0.5.24

• 🎨 Marketplace Branding Refresh: keeper icon 與 VSX banner 改為新的系列化品牌視覺，對齊 Academic Figures MCP / MedPaper Assistant 的產品語言
• 🔐 OpenAlex API Key Support: extension 新增 zoteroMcp.openAlexApiKey 設定，會將 OPENALEX_API_KEY 傳給 PubMed Search MCP
• 🔄 Bundled Asset Refresh: extension 重新同步最新 pubmed-search-mcp agents / hooks / skills，並更新到包含修正 os import 的版本
• PubMed Search baseline upgraded to 0.5.4: embedded environment now requires pubmed-search-mcp>=0.5.4, and startup now injects PUBMED_WORKSPACE_DIR to avoid VS Code regressions.
• Fixed PubMed package source: embedded/manual 安裝改用已修正的 upstream snapshot，避免直接安裝有問題的 0.5.4 PyPI 套件

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)
• PDF attachment access (list attachments, get indexed fulltext)

🔍 PubMed Search (v0.5.6)

• 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 or 8 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, fixed pubmed-search-mcp snapshot)
   • Register MCP servers with VS Code
   • Install official Copilot instructions, workflow guides, @research agent, and collaboration hook assets

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

🎯 Assistant Research Assets

The extension installs workflow guides that teach Copilot and Cline:

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 Official Assistant Assets 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 the fixed pubmed-search-mcp snapshot (10-100x faster than pip)
4. MCP Servers: Starts both servers and registers with VS Code
5. Assistant Assets: 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 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 Official Assistant Assets 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.