Agent skill

Figure Reference Checker

by aipoch in aipoch/medical-research-skills

Use figure reference checker for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries.

MITAuto-check passedResearch & Science

Install Figure Reference Checker

skills CLI
$ npx skills add aipoch/medical-research-skills --skill figure-reference-checker -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install aipoch/medical-research-skills figure-reference-checker --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/'scientific-skills/Academic Writing/figure-reference-checker' .claude/skills/figure-reference-checker && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
figure-reference-checker
GitHub stars
2k
Token cost
~2k tokens
SKILL.md length
944 words
Files
5 (incl. scripts, references)
Skills in repo
567
Repo updated
First seen
Licence
MIT

At a glance

Use figure reference checker for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries.

  • Works in 5 steps: Confirm the user objective, required… → Validate that the request matches the… → Use the packaged script path or the… → …
  • Tasks that involve Scientific writing
  • SKILL.md covers Quick Check, Audit-Ready Commands, When to Use and Workflow, plus 19 more sections
  • Runs Python scripts from its folder; calls python

What it does

Figure Reference Checker is an agent skill from aipoch/medical-research-skills. Use figure reference checker for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries.

Its SKILL.md is about 2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 6 other files, including scripts and reference files (for example `POLISH_CHANGELOG.md`, `eval_report_figure-reference-checker_result.json` and `references/audit-reference.md`).

It sits in Research & Science, covering Scientific writing. The repository describes itself as: Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing. The licence is MIT.

When your agent uses it

  • Tasks that involve Scientific writing

Example prompts

  • “/figure-reference-checker”

Requirements

  • Python 3

Workflow steps

5 steps, taken from the first numbered list in SKILL.md.

  1. Confirm the user objective, required inputs, and non-negotiable constraints before doing detailed work.
  2. Validate that the request matches the documented scope and stop early if the task would require unsupported assumptions.
  3. Use the packaged script path or the documented reasoning path with only the inputs that are actually available.
  4. Return a structured result that separates assumptions, deliverables, risks, and unresolved items.
  5. If execution fails or inputs are incomplete, switch to the fallback path and state exactly what blocked full completion.

What it can do on your machine

Read from SKILL.md and the folder at commit 686e09d. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships 1 file in scripts/ (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Figure Reference Checker loads about 2k tokens when it runs, and up to ~2.1k if it reads all its reference files. Until then it costs about 42 tokens; SKILL.md has 944 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~42
When it runs · the whole SKILL.md, loaded when a task matches
~2k
With references · SKILL.md plus every file in references/, read only if the agent opens them
~2.1k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 944 words, ~1,972 tokens.

Download SKILL.mdSave it as .claude/skills/figure-reference-checker/SKILL.md (or your agent's skills folder). This skill also uses 4 other files; get the full folder from GitHub.
name
figure-reference-checker
description
Use figure reference checker for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries.
license
MIT
author
AIPOCH

Source: https://github.com/aipoch/medical-research-skills

Figure Reference Checker

Check consistency of figure references in manuscripts.

Quick Check

Use this command to verify that the packaged script entry point can be parsed before deeper execution.

bash
python -m py_compile scripts/main.py

Audit-Ready Commands

Use these concrete commands for validation. They are intentionally self-contained and avoid placeholder paths.

bash
python -m py_compile scripts/main.py
python scripts/main.py --help

When to Use

  • Use this skill when the task needs Use figure reference checker for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries.
  • Use this skill for academic writing tasks that require explicit assumptions, bounded scope, and a reproducible output format.
  • Use this skill when you need a documented fallback path for missing inputs, execution errors, or partial evidence.

Workflow

  1. Confirm the user objective, required inputs, and non-negotiable constraints before doing detailed work.
  2. Validate that the request matches the documented scope and stop early if the task would require unsupported assumptions.
  3. Use the packaged script path or the documented reasoning path with only the inputs that are actually available.
  4. Return a structured result that separates assumptions, deliverables, risks, and unresolved items.
  5. If execution fails or inputs are incomplete, switch to the fallback path and state exactly what blocked full completion.

Parameters

ParameterTypeDefaultRequiredDescription
--manuscript, -mstring-YesPath to manuscript file

Usage

text
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

Output Requirements

Every final response should make these items explicit when they are relevant:

  • Objective or requested deliverable
  • Inputs used and assumptions introduced
  • Workflow or decision path
  • Core result, recommendation, or artifact
  • Constraints, risks, caveats, or validation needs
  • Unresolved items and next-step checks

Error Handling

  • If required inputs are missing, state exactly which fields are missing and request only the minimum additional information.
  • If the task goes outside the documented scope, stop instead of guessing or silently widening the assignment.
  • If scripts/main.py fails, report the failure point, summarize what still can be completed safely, and provide a manual fallback.
  • Do not fabricate files, citations, data, search results, or execution outcomes.

Input Validation

This skill accepts requests that match the documented purpose of figure-reference-checker and include enough context to complete the workflow safely.

Do not continue the workflow when the request is out of scope, missing a critical input, or would require unsupported assumptions. Instead respond:

figure-reference-checker only handles its documented workflow. Please provide the missing required inputs or switch to a more suitable skill.

References

Show full SKILL.md (377 more words)Show less

Response Template

Use the following fixed structure for non-trivial requests:

  1. Objective
  2. Inputs Received
  3. Assumptions
  4. Workflow
  5. Deliverable
  6. Risks and Limits
  7. Next Checks

If the request is simple, you may compress the structure, but still keep assumptions and limits explicit when they affect correctness.

When Not to Use

  • Do not proceed when required input files, identifiers, parameters, or context are missing — ask the user to provide them first.
  • Do not assume capabilities beyond this skill's declared scope when the user requests external operations or inferences.
  • Do not proceed without user confirmation when overwriting existing results, executing high-cost batch operations, or expanding task scope.

Required Inputs

FieldRequiredFormat/SourceExampleIf Missing
User task descriptionYesTextResearch question, writing goal, analysis objectiveStop and ask user to provide
Primary input materialDepends on taskText, file path, ID, table, or literaturePMID, PDF, CSV, DOCX, keywords, etc.Specify which material type is missing
Output preferenceNoTextLanguage, format, target journal, templateUse skill default format

Output Contract

  • Primary output: Structured result or target file aligned with this skill's objective.
  • Optional output: Intermediate check notes, issue list, supplementary suggestions, or generated file paths.
  • Format requirement: Unless the user specifies otherwise, prefer stable, reviewable Markdown or JSON; if the skill's bundled script requires a fixed format, use that format.
  • If partially complete: Must explicitly mark as PARTIAL and state which steps are completed and which remain.

Failure Handling

  • Missing critical input: Explicitly state which fields, files, or identifiers are missing and pause.
  • Script, template, or resource execution failure: Report the failing step, likely cause, and recovery suggestions — do not silently degrade.
  • Partial completion only: Return the verified portion first, then list remaining blockers and suggested next steps.

User Checkpoints

  • Before executing batch processing, overwriting files, long-running searches, or multi-stage generation, confirm scope and output format with the user.
  • Before proceeding when a key judgment is ambiguous, evidence is insufficient, or the workflow is entering the next stage, confirm with the user.

Quick Validation

  • Check that key scripts, templates, or reference file paths this skill depends on exist.
  • Check that the final output contains the core fields, sections, or files specified for this task.
  • Check that results clearly mark assumptions, limitations, and incomplete items.

© aipoch, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 4 other files (scripts, references) in scientific-skills/Academic Writing/figure-reference-checker of aipoch/medical-research-skills.

  • SKILL.md
  • POLISH_CHANGELOG.md
  • eval_report_figure-reference-checker_result.json
  • references/audit-reference.md
  • scripts/main.py

Open the folder on GitHubat commit 686e09d

Compare with similar skills

Figure Reference Checker next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Figure Reference Checker compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Figure Reference Checker this skillaipoch/medical-research-skills2k—~2kAutomated safety check: PassMIT
Citation Verification GuideGalaxy-Dawn/claude-scholar5.7k3 repos~1.9kAutomated safety check: PassMIT
Nature-Style Scientific FiguresYuan1z0825/nature-skills46k—~2.9kAutomated safety check: PassApache-2.0
Citation ManagementK-Dense-AI/claude-scientific-writer2.4k3 repos~3.9kAutomated safety check: NotesMIT
Academic Paper Composerlishix520/academic-paper-skills1.4k2 repos~6.3kAutomated safety check: PassMIT
Academic Paper Writing PipelineImbad0202/academic-research-skills51k—~16kAutomated safety check: PassCustom licence

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Questions about Figure Reference Checker

What does Figure Reference Checker do?

Use figure reference checker for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries. Figure Reference Checker is an agent skill from aipoch/medical-research-skills. Use figure reference checker for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries.

When should I use Figure Reference Checker?

Figure Reference Checker fits situations like: tasks that involve Scientific writing.

How do I install Figure Reference Checker in Claude Code?

Run `npx skills add aipoch/medical-research-skills --skill figure-reference-checker -a claude-code`. Or copy the skill folder (scientific-skills/Academic Writing/figure-reference-checker in aipoch/medical-research-skills) into .claude/skills/figure-reference-checker in your project. Claude Code loads it when a task matches its description.

How do I install Figure Reference Checker in Codex?

Run `npx skills add aipoch/medical-research-skills --skill figure-reference-checker -a codex`. Or copy the skill folder (scientific-skills/Academic Writing/figure-reference-checker in aipoch/medical-research-skills) into .agents/skills/figure-reference-checker in your project. Codex loads it when a task matches its description.

Can I use Figure Reference Checker in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add aipoch/medical-research-skills --skill figure-reference-checker -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/figure-reference-checker, .gemini/skills/figure-reference-checker, .github/skills/figure-reference-checker and .opencode/skills/figure-reference-checker in your project.

What does Figure Reference Checker need to run?

Going by SKILL.md and its folder, Figure Reference Checker needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.

Does Figure Reference Checker access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Figure Reference Checker safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Figure Reference Checker use?

Figure Reference Checker is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Figure Reference Checker use?

About 2k tokens (SKILL.md is roughly 7.9k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 178 tokens, read only when the agent opens those files.

What are the alternatives to Figure Reference Checker?

Skills that share tags, products or a category with Figure Reference Checker: Citation Verification Guide (Galaxy-Dawn/claude-scholar, 5.7k stars), Nature-Style Scientific Figures (Yuan1z0825/nature-skills, 46k stars), Citation Management (K-Dense-AI/claude-scientific-writer, 2.4k stars) and Academic Paper Composer (lishix520/academic-paper-skills, 1.4k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Figure Reference Checker?

aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,974 GitHub stars. The repository holds 567 skills in this directory. The repository was last updated on September 17, 2026.

Source: aipoch/medical-research-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.