dengls24/annota

**Turn your PDF library into an intelligent research assistant.**
AI reads your papers, highlights key findings, explains formulas, and writes structured notes — all saved back to your reference manager.
Features · Quick Start · Usage Examples · Screenshots · Roadmap
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What Can It Do?
| You say... | AI does... |
|------------|------------|
| "高亮摘要中的发现结果" (Highlight findings in the abstract) | Reads the abstract, identifies findings, highlights them in green |
| "解释第3页的公式" (Explain the formulas on page 3) | Extracts the formula, adds an explanation as a note annotation |
| "写一份结构化阅读笔记" (Write a structured reading note) | Generates a note with contributions, methods, results, limitations — saved to your library |
| "以 MICRO 审稿人视角审阅" (Review as a MICRO reviewer) | Produces a structured review with scores and actionable feedback |
AI reads the paper → understands content → creates precise annotations
*AI generates a structured reading summary with key findings, methods, and conclusions*
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✨ Features
9 MCP Tools
| Tool | What it does |
|------|-------------|
| search_zotero_items | Search by title / author / key |
| list_zotero_items | Browse recent items |
| get_item_metadata | Get authors, year, venue, DOI |
| get_pdf_text_bulk | Extract full text (no coords, fast) |
| get_pdf_layout_text | Extract text + precise coordinates |
| list_annotations | View existing annotations |
| create_pdf_annotation | Create highlight / underline |
| batch_annotate | Create multiple annotations at once |
| add_child_note | Add a note to any item |
3 Claude Code Skills (Slash Commands)
| Command | Function |
|---------|----------|
| /annota-annotate | Smart annotation with semantic color coding |
| /annota-summarize | Structured reading notes saved to your library |
| /annota-review | Simulated peer review with scoring rubric |
Smart Design
- **Two-phase workflow** — Reads full text first (cheap), then only gets coordinates for target sentences (precise). Reduces context usage by 63–80%.
- **Auto-skip references** — Detects "References" section and skips it. A 21-page paper extracts only 13 pages.
- **Batch annotations** — Creates 10 highlights in 1 API call instead of 10.
- **Friendly errors** — Write failures return helpful messages instead of crashing.
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🚀 Quick Start (3 Minutes)
Step 1: Clone & Install
Step 2: Configure Claude Code
Add to ~/.claude.json (or via Claude Code Settings > MCP Servers):
**Windows:**
**macOS / Linux:**
> **Finding your Zotero data directory:**
> - **Windows**: Zotero → Edit → Settings → Advanced → Data Directory Location (default: C:\Users\YourName\Zotero)
> - **macOS**: Zotero → Settings → Advanced → Data Directory Location (default: ~/Zotero)
> - **Linux**: default ~/Zotero
Step 3: Use It
Just talk to Claude naturally:
Or use slash commands:
> **macOS path tip:** Drag a file from Finder into the terminal to get its full path, or right-click → "Copy as Pathname".
(Optional) Install Skills Globally
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📖 Usage Examples
Example 1: Highlight Key Findings
**Input:**
**Result:**
*AI identifies findings in the abstract and highlights them in green*
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Example 2: Annotate Hypotheses & Theories
**Input:**
**Result:**
*Hypotheses highlighted in yellow, with Chinese explanation notes for the underlying theory*
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Example 3: Explain Formulas
**Input:**