version: "1.0.1" name: paper-review-helper description: Copilot for scientific paper review. Use when reviewing a research paper (PDF/LaTeX), guiding section-by-section analysis, logging issues, and generating structured review responses. argument-hint: <path-to-pdf-or-folder> allowed-tools:

• Read
• Write
• Bash
• Glob
• Grep
• WebSearch
• WebFetch
• AskUserQuestion

Paper Review Helper

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

Phase 1: Setup

1. 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."

1. 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.

1. Initialize workspace:

<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:

1. Chunk appropriately:

• Section ≤5 paragraphs: review whole
• Section >5 paragraphs: split by \subsection or paragraph groups

1. Present section with:
2. Section text - save the partial tex to markdown format.
3. Inline markers for issues (see Grammar Check Markers) in the markdown file.
4. and provide the user with a path link to the file in the workspace.
5. Figure refs: [Figure X: images/<filename> - <caption>] with a path link to the file in the workspace.

1. Ask user via AskUserQuestion:

• "Questions about this section?"
• "Any concerns or unclear points?"
• "Rate clarity: clear / somewhat unclear / confusing"

1. 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

1. Log to artifact/review-log.md:

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

1. 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

1. Gather context via AskUserQuestion:

• "Overall impression? (accept / minor revision / major revision / reject)"
• "Editor's specific questions?"
• "Journal level? (top-tier / mid-tier / specialized)"

1. Generate review to artifact/REVIEW.md:

# 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