Paper Review

Step 0: Detect Input Type

Determine the input type from $ARGUMENTS:

if starts with "10." or "doi:" → DOI mode
if starts with "http" → URL mode
if matches "(Paper)" or exists as vault .md file → Vault note mode
else → Zotero search mode

DOI Mode

1. Resolve DOI via WebFetch: https://doi.org/[DOI]
2. Extract metadata (title, authors, abstract, journal)
3. If PDF available (open access / arXiv), read it
4. If paywalled, work with abstract + any available metadata
5. Check if paper already exists in Zotero → if yes, switch to Zotero mode
6. Skip to Step 3 (Load Paper Metadata)

URL Mode

1. Fetch content via WebFetch or Playwright (for JS-rendered pages)
2. Extract metadata from the page
3. If arXiv: also fetch PDF via Read tool
4. Skip to Step 3

Vault Note Mode

1. Read the existing vault note
2. Extract metadata from frontmatter (title, DOI, source, tags)
3. If DOI exists in frontmatter, optionally fetch full paper for deeper review
4. Skip to Step 5 (present briefing based on existing note content + any new data)

Zotero Search Mode (original behavior)

Continue to Step 1 below.

Step 1: Locate Zotero Data Directory

Detect the Zotero data directory automatically based on the OS:

OS="$(uname -s)"
case "$OS" in
  Linux*)
    if grep -qi microsoft /proc/version 2>/dev/null; then
      WIN_USER=$(cmd.exe /C "echo %USERNAME%" 2>/dev/null | tr -d '\r')
      ZOTERO_DIR="/mnt/c/Users/${WIN_USER}/Zotero"
    else
      ZOTERO_DIR="$HOME/Zotero"
    fi
    ;;
  Darwin*)
    ZOTERO_DIR="$HOME/Zotero"
    ;;
esac

If the directory is not found at the expected location, search for zotero.sqlite under the user's home directory to locate it.

Step 2: Search Zotero Database

Query zotero.sqlite to find matching papers. Search across titles, creators, and collection names. If multiple results are found, present a numbered list and ask the user to choose.

Step 3: Load Paper Metadata

For the selected paper, extract full metadata: title, authors, date, DOI, journal, abstract, tags, and PDF attachment path.

The PDF path format is storage:filename.pdf. The actual file is at: {ZOTERO_DIR}/storage/{attachment_key}/{filename}

Step 4: Read the PDF

Use the Read tool to read the PDF file. Focus on extracting:

• Abstract
• Introduction (research gap and motivation)
• Methodology (key approach)
• Results (main findings)
• Discussion and Conclusions

Step 5: Present Briefing and Start Discussion

Present a structured briefing to the user:

## [Paper Title]
**Authors:** [list] | **Year:** [year] | **Journal:** [journal]

### One-line Summary
[What this paper does in one sentence]

### Key Contributions (3 items max)
1. ...
2. ...
3. ...

### Methodology
[Brief description of the approach]

### Limitations
- [Author-acknowledged limitations]
- [Your observed limitations]

---

### Discussion Topics
I'd like to discuss these aspects with you:

1. **[Topic 1]** — [Why this is interesting/debatable]
2. **[Topic 2]** — [Connection to your research area]
3. **[Topic 3]** — [Potential gap or extension]

Which topic interests you, or do you have your own topic to start with?

Step 6: Interactive Discussion

After presenting the briefing, engage in natural conversation. Both you and the user can propose new discussion topics. Continue until the user indicates the discussion is complete (e.g., "done", "save", "끝", "저장", or moves to a new task).

Step 7: Auto-Save Note (after discussion ends)

When the discussion concludes, automatically create a review note:

7-1. Read Tag Taxonomy

Read 99-meta/tag-taxonomy.md from the vault and select 3-6 appropriate tags.

7-2. Search for Related Notes

Search the Obsidian vault for related notes by key terms from the paper. Suggest 2-5 wikilinks.

7-3. Create the Note (07-wiki/paper-notes/ REQUIRED)

IMPORTANT (2026-04-15 update): Paper notes are interpreted data and MUST be saved to 07-wiki/paper-notes/, NOT 01-inbox/ or 08-raw/. See 07-wiki/_protocol.md and 08-raw/_protocol.md.

Save to 07-wiki/paper-notes/ with filename format: {FirstAuthor}{Year}.md (e.g., Kim2024.md, Hao2025.md, Chaboche1988b.md).

중복 체크 필수: 생성 전 ls 07-wiki/paper-notes/{AuthorYear}*.md 확인. 이미 있으면 update 로 전환 (overwrite 금지, append/merge).

Note template:

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