Annotate Research Papers
Writes study notes, highlights and figure comments into a paper's PDF through Zotero.
Install
npx skills add 54yyyu/zotero-mcp --skill annotate-paper -g -a claude-code -y- Repository
- 54yyyu/zotero-mcp5.7k
- Category
- Writing
- Updated
- 4d ago
- License
- MIT
- Context cost
- Lightabout 1,439 tokens
- Runs scripts
- No, instructions only
What it does
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.
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:
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
zotero-cli read ITEM_KEY --start-page 1 --end-page 99
