figure-reference-checker
npx machina-cli add skill aipoch/medical-research-skills/figure-reference-checker --openclawFigure Reference Checker
Check consistency of figure references in manuscripts.
Parameters
| Parameter | Type | Default | Required | Description |
|---|---|---|---|---|
--manuscript, -m | string | - | Yes | Path to manuscript file |
Usage
python scripts/main.py --manuscript paper.docx
Features
- Detect orphaned figure references
- Check figure-label consistency
- Flag missing citations
Risk Assessment
| Risk Indicator | Assessment | Level |
|---|---|---|
| Code Execution | Python/R scripts executed locally | Medium |
| Network Access | No external API calls | Low |
| File System Access | Read input files, write output files | Medium |
| Instruction Tampering | Standard prompt guidelines | Low |
| Data Exposure | Output files saved to workspace | Low |
Security Checklist
- No hardcoded credentials or API keys
- No unauthorized file system access (../)
- Output does not expose sensitive information
- Prompt injection protections in place
- Input file paths validated (no ../ traversal)
- Output directory restricted to workspace
- Script execution in sandboxed environment
- Error messages sanitized (no stack traces exposed)
- Dependencies audited
Prerequisites
No additional Python packages required.
Evaluation Criteria
Success Metrics
- Successfully executes main functionality
- Output meets quality standards
- Handles edge cases gracefully
- Performance is acceptable
Test Cases
- Basic Functionality: Standard input → Expected output
- Edge Case: Invalid input → Graceful error handling
- Performance: Large dataset → Acceptable processing time
Lifecycle Status
- Current Stage: Draft
- Next Review Date: 2026-03-06
- Known Issues: None
- Planned Improvements:
- Performance optimization
- Additional feature support
Source
git clone https://github.com/aipoch/medical-research-skills/blob/main/scientific-skills/Academic writing/figure-reference-checker/SKILL.mdView on GitHub Overview
The figure-reference-checker validates consistency of figure references in manuscripts. It detects orphaned references, ensures label consistency, and flags missing citations to improve accuracy before submission.
How This Skill Works
Run the Python script with a manuscript path (--manuscript). The tool scans the document, extracts figure labels and references, cross-checks them for consistency, and outputs a report highlighting issues.
When to Use It
- Preparing final draft for submission
- Auditing a manuscript with many figures
- Collaborating with co-authors to fix cross-references
- After edits to ensure no broken references
- Prior to grant or proposal submissions
Quick Start
- Step 1: Run: python scripts/main.py --manuscript paper.docx
- Step 2: Open and review the generated figure-ref report
- Step 3: Fix references in the manuscript and re-run to verify
Best Practices
- Run on a clean copy of the manuscript
- Use a consistent labeling scheme for figures and references
- Review the generated report to fix orphan references
- Verify figure numbers and labels match across text and captions
- Re-run after fixes to confirm all references are resolved
Example Use Cases
- Manuscript with an orphaned reference where Fig. 5 is cited but not labeled
- Inconsistent labeling like Figure 2 in text but Fig. 3 in captions
- Missing citations for newly added figures during revision
- Large multi-section manuscript with hundreds of figures and cross-references
- Post-edit manuscript where renumbered figures created mismatches
Frequently Asked Questions
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