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figure-reference-checker

npx machina-cli add skill aipoch/medical-research-skills/figure-reference-checker --openclaw
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SKILL.md
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Figure Reference Checker

Check consistency of figure references in manuscripts.

Parameters

ParameterTypeDefaultRequiredDescription
--manuscript, -mstring-YesPath 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 IndicatorAssessmentLevel
Code ExecutionPython/R scripts executed locallyMedium
Network AccessNo external API callsLow
File System AccessRead input files, write output filesMedium
Instruction TamperingStandard prompt guidelinesLow
Data ExposureOutput files saved to workspaceLow

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

  1. Basic Functionality: Standard input → Expected output
  2. Edge Case: Invalid input → Graceful error handling
  3. 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

  1. Step 1: Run: python scripts/main.py --manuscript paper.docx
  2. Step 2: Open and review the generated figure-ref report
  3. 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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