Paper Review Helper

Name: paper-review-helper
Rating: 92
Author: caidish

Guide user through structured paper review, logging issues and generating formal review response.

Phase 1: Setup

•
Locate paper from $ARGUMENTS:
- •If PDF file: create <paper-name>-review/ folder, copy PDF into it
- •If folder: search for .tex first (prioritize over PDF)
- •No paper found → AskUserQuestion: "No paper detected. Please provide path to paper."
•
Convert PDF → LaTeX (if no .tex exists):
bash
```
# Check credentials
[ -n "$MATHPIX_APP_ID" ] && [ -n "$MATHPIX_API_KEY" ] && echo "OK" || echo "MISSING"
```
- •If MISSING → notify user: "Set MATHPIX_APP_ID and MATHPIX_API_KEY for PDF→LaTeX. Proceeding with direct PDF (figures not extractable)."
- •If OK → run conversion:
bash
```
python ~/.claude/plugins/science-skill/skills/paper-review-helper/scripts/pdf2tex.py "<pdf_path>" "<paper-folder>"
```
Output structure: <paper-folder>/<pdf_id>/<pdf_id>.tex with images/ subfolder for figures.
•
Initialize workspace:

text

<paper-folder>/
├── <pdf_id>/                 # Mathpix output (if converted)
│   ├── <pdf_id>.tex          # Converted LaTeX
│   └── images/               # Extracted figures
├── artifact/
│   ├── review-log.md         # Conversation log
│   ├── issues-major.md       # Major issues
│   ├── issues-minor.md       # Minor issues
│   └── programs/             # Math verification scripts
└── original.pdf              # Source PDF (if applicable)

Phase 2: Section-by-Section Review

Parse LaTeX structure: \section, \subsection, \begin{abstract}. For each section:

•
Chunk appropriately:
- •Section ≤5 paragraphs: review whole
- •Section >5 paragraphs: split by \subsection or paragraph groups
•
Present section with:
1. •Section text - save the partial tex to markdown format.
2. •Inline markers for issues (see Grammar Check Markers) in the markdown file.
3. •and provide the user with a path link to the file in the workspace.
4. •Figure refs: [Figure X: images/<filename> - <caption>] with a path link to the file in the workspace.
•
Ask user via AskUserQuestion:
- •"Questions about this section?"
- •"Any concerns or unclear points?"
- •"Rate clarity: clear / somewhat unclear / confusing"
•
Respond to requests:
- •Citations: WebSearch for DOI, author names, paper titles
- •Background: WebSearch, WebFetch for concepts
- •Math check: write script to artifact/programs/, run with Python/SymPy
- •Figures: read from images/ folder, describe or use /vision skill
•
Log to artifact/review-log.md:

markdown

## [Section Name] - [Timestamp]
### User Questions
- Q: ...
- A: ...
### Issues Identified
- [MAJOR] ...
- [MINOR] ...
### Tools Used
- WebSearch: "query" → finding

•
Classify issues:
- •Major → issues-major.md: methodology flaws, unsupported claims, logical errors
- •Minor → issues-minor.md: grammar, typos, unclear wording

Skip Supplementary/Appendix unless user requests.

Phase 3: Review Generation

•
Gather context via AskUserQuestion:
- •"Overall impression? (accept / minor revision / major revision / reject)"
- •"Editor's specific questions?"
- •"Journal level? (top-tier / mid-tier / specialized)"
•
Generate review to artifact/REVIEW.md:

markdown

# Review of [Paper Title]

## Summary
[1-2 sentences]

## Overall Recommendation
[User's decision + justification]

## Major Issues
1. **Issue**: [description]
   - **Location**: Section X, paragraph Y / Equation N
   - **Impact**: [why this matters]
   - **Suggestion**: [fix or note if unfixable]

## Minor Issues
[Grouped by type: grammar, clarity, formatting]

## User Misunderstandings Analysis
[If user had confusion during review:]
- **Confusion**: [what]
- **Cause**: paper vagueness / reader knowledge gap
- **Recommendation**: [should paper clarify?]

## Constructive Feedback
[Positives + specific improvements]

## Editor Questions Response
[If provided]

Grammar Check Markers

Inline markers when presenting text:

•[G: ...] - grammar error
•[C: ...] - clarity issue
•[?] - ambiguous/unsupported claim
•[REF?] - missing or questionable citation
•[EQ?] - equation to verify