---
name: paper_review
description: Thoroughly review an academic paper and create a structured Markdown note using the note_template.md. Use when the user asks to review, read, summarise, or take notes on a paper.
---

# Paper Review

## Overview

Produce a thorough, structured literature note for the indicated paper. The note is filled **exclusively from the paper itself** — do not introduce any external information, prior knowledge, or internet sources. Every claim in the note must be traceable to the paper.

## Input

`ARGUMENTS` may be:
- A file path to a PDF (absolute or relative)
- A Zotero storage key (e.g. `23SUA9S3`) — the PDF lives at `~/Zotero/storage/<KEY>/*.pdf`
- A keyword/title to search in `~/Zotero/storage/` using Glob

## Instructions

### Step 1 — Locate the PDF

- If a direct path is given, use it.
- If a Zotero key is given, Glob `~/Zotero/storage/<KEY>/*.pdf`.
- If a title/keyword is given, Glob `~/Zotero/storage/**/*.pdf` and find the closest match. If multiple candidates exist, list them and ask the user to confirm before proceeding.

### Step 2 — Read the PDF

- Use the Read tool with `pages:` parameter.
- **First read pages 1–5** to extract metadata (title, authors, year, journal, DOI, abstract).
- Then read the full paper in **chunks of up to 20 pages** until the entire document is covered.
- Keep a running internal summary after each chunk — do not lose content from earlier chunks.
- For short papers (≤ 20 pages), read in a single call.

### Step 3 — Fill the note template

Read `note_template.md` (in the same folder as this SKILL.md) and fill every field strictly from the paper:

| Field | Source in paper |
|---|---|
| `{{title}}` | Title page / header |
| `{{authors}}` | Author list |
| `{{year}}` | Publication year |
| `{{citekey}}` | Derive as `AuthorYEAR` (e.g. `Acemoglu2012`) |
| `{{tags}}` | Infer 2–4 topic tags from content (e.g. `IP-finance, Basel-III`) |
| `{{date}}` | Today's date in YYYY-MM-DD |
| `{{publicationTitle}}` | Journal/conference name |
| `{{DOI}}` | DOI if present, else `N/A` |
| `{{abstractNote}}` | Verbatim or lightly condensed abstract |
| `{{annotations}}` | Key quoted passages with page numbers |
| `{{id}}` | Zotero key if known, else leave blank |
| `{{pdfLink}}` | Absolute path to the PDF |

Fill the analytical sections from your reading:

- **Key Takeaways** — 3–5 bullet points: the most important insights a reader must retain
- **Summary** — 2–4 paragraph narrative of what the paper does and why
- **Methodology** — Approach, data sources, analytical methods used
- **Main Findings** — Numbered list of empirical or theoretical results
- **Connections** — What the paper supports, contradicts, extends (infer from paper's own literature discussion only)
- **Personal Thoughts** — Leave as empty bullet (`-`) — the user fills this
- **Questions** — 2–3 open questions that arise from reading the paper
- **Reading Progress** — Tick all checkboxes that were covered during this review

### Step 4 — Save the note

Generate the filename as: `citekey.md` (e.g. `Acemoglu2012.md`)

Save the completed note to **both** locations without asking for permission:

1. **Obsidian inbox** (always):
   `/Users/michal/Library/Mobile Documents/iCloud~md~obsidian/Documents/Michal/Research/00_Inbox/<citekey>.md`

2. **Project literature folder** (always):
   Detect the current project from the working directory or the path of the PDF. If the PDF is under `projects/<project_name>/`, save to `projects/<project_name>/literature/<citekey>.md`. If no project context is clear, save to `projects/literature/<citekey>.md`.
   Create the `literature/` folder if it does not exist.

### Step 5 — Report to user

After saving, report:
- Citekey and title
- Final note path(s)
- Any fields that could not be filled (e.g. DOI not found in paper)

## Rules

- **Paper only.** Do not add information that is not explicitly stated in the paper. If a field cannot be determined from the paper, write `N/A` or leave blank.
- **No internet.** Do not use WebSearch or WebFetch to look up the paper.
- **No permission prompts** for saving to the Obsidian inbox or the project literature folder.
- For very long papers (> 60 pages), prioritise: abstract, introduction, methodology, results, conclusion — but still attempt all sections.

## ARGUMENTS: $ARGUMENTS