# Annotate Research Papers

Writes study notes, highlights and figure comments into a paper's PDF through Zotero.

- Repository: https://github.com/54yyyu/zotero-mcp (5680 stars)
- Category: Writing
- License: MIT
- Last updated: 2026-11-01
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add 54yyyu/zotero-mcp --skill annotate-paper -g -a claude-code -y`
Codex: `npx skills add 54yyyu/zotero-mcp --skill annotate-paper -g -a codex -y`
Cursor: `npx skills add 54yyyu/zotero-mcp --skill annotate-paper -g -a cursor -y`
Gemini CLI: `npx skills add 54yyyu/zotero-mcp --skill annotate-paper -g -a gemini-cli -y`

## Description

Read the open paper and write study annotations into its PDF with zotero-cli - a context box on the title, a four-part summary on the abstract, role-coded abstract highlights, one box per figure panel with a teaching comment, colour-coded body highlights, and a reading note. Use when asked to "annotate", "read and annotate", or "help me understand" a paper.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# Annotate a paper for understanding

The goal is a PDF someone can study from cold: the background, the argument and every figure explained in place.

## Colour scheme (change it here)

Use exactly these colours so every paper reads the same way. Edit the table to make the scheme your own; the rest
of the skill refers to the roles, not the colours.

| Annotation | Where | Colour | Content |
|---|---|---|---|
| Context box | around the title and authors, page 1 | orange | What a newcomer needs first: the field, key terms defined plainly, the problem's history, why this approach. Start with `CONTEXT`. |
| Four-part summary | around the abstract | magenta | `THE WHOLE PAPER IN FOUR PARTS.` then `// PROBLEM:`, `// METHOD:` (with the real numbers), `// RESULTS:` (numbered), `// TAKEAWAY:` and the limits. |
| Abstract highlights | sentences in the abstract | by role | Prefix each comment with its role: `PROBLEM.` / `GOAL.` / `CONCLUSION.` (yellow), `METHOD.` (blue), `DISCOVERY.` (green). |
| Figure boxes | one per sub-panel | purple | See "Figure boxes" below. |
| Body highlights | key sentences throughout | yellow / blue / green / red | yellow = claim or big idea; blue = method, data or design choice; green = finding or evidence; red = limitation, caveat or critique. |

This skill sits on top of the `zotero-cli` skill. Run `zotero-cli config` once first; writing annotations needs local
write access.

## 1. Find the paper and its PDF

Use the paper that is open in the reader, or the one the user names:

```bash
zotero-cli --json search "title words" --limit 5
zotero-cli --json get children ITEM_KEY          # the PDF attachment's key; supplementary PDFs are attachments too
```

Annotate the main PDF, not the supplement, unless asked.

## 2. Read the whole paper, then look at every figure

```bash
zotero-cli read ITEM_KEY --start-page 1 --end-page 99
```

The rest: https://github.com/54yyyu/zotero-mcp/blob/HEAD/docs/skills/annotate-paper/SKILL.md