Result Figure Consistencycheck

---
name: result-figure-consistencycheck
description: Checks consistency between paper result descriptions and figure legends (text-only) when the input is a PDF-to-Markdown full text containing page breaks (e.g., `## Page XX`) and legend text; outputs a Markdown consistency report and a UTF-8 CSV issue list.
license: MIT
author: AIPOCH
---
> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)


## When to Use

- You converted a paper PDF to Markdown and need to verify that **Results text** matches **figure legends** (without inspecting the images).
- You want to detect **missing figure references** in the Results section (e.g., a legend describes an analysis not mentioned in text).
- You need to find **numerical/label mismatches** (e.g., group names, time points, units, n-values) between Results paragraphs and legends.
- You are preparing a revision and want an **actionable discrepancy list** down to the **panel/sub-figure** level.
- You need standardized outputs (Markdown report + CSV) for editorial or QA workflows.

## Key Features

- Compares **Results descriptions** vs **figure legend text** using the PDF-to-Markdown source (including `## Page XX` markers).
- Produces:
  - A **Markdown consistency report** (UTF-8).
  - A **CSV issue list** (UTF-8) with structured fields for tracking and revision.
- Enforces a **template-based report format** using `assets/consistency_template.md`.
- Uses a **rule/checklist reference** from `references/guide.md`.
- Text-only validation: **does not read figure images** and **does not infer visual content**.

## Dependencies

- None (no external runtime dependencies specified).
- Input prerequisite (if starting from PDF): a PDF-to-Markdown conversion step (e.g., `pdf-extract`) must be completed before running this check.

## Example Usage

### Input

Place the converted full text Markdown in your working location (example: `inputs/paper_fulltext.md`). The file should include page headers like:

```md
## Page 12
... Results text ...

Figure 3. ...
(A) ...
(B) ...
```

### Run (conceptual workflow)

1. Read the full Markdown input (PDF conversion output).
2. Identify:
   - Result paragraphs describing findings.
   - Figure legend blocks (including panel labels such as A/B/C).
3. Compare legend statements against Results statements and record discrepancies.
4. Write outputs to `outputs/`:
   - `outputs/consistency_report.md` (UTF-8)
   - `outputs/consistency_issues.csv` (UTF-8)

### Output files

**`outputs/consistency_issues.csv`** (UTF-8) columns:

```csv
Figure Number,Location/Reference,Issue Description,Suggested Revision,Priority
```

Notes:
- `Location/Reference` must contain only `Page XX`.
- Issues should be granular to the **panel/sub-figure** level when applicable.

**`outputs/consistency_report.md`** (UTF-8) must follow:

- Template: `assets/consistency_template.md`
- If no issues are found, write **"None found"** in the relevant sections.

## Implementation Details

- **Scope of comparison**
  - Only compare **main text Results descriptions** and **figure legend text** present in the Markdown input.
  - Do **not** inspect images or infer information not explicitly stated in text.

- **Rules and checklist**
  - Follow the specific checking rules and required output points defined in:
    - `references/guide.md`

- **Report formatting**
  - The Markdown report must be generated by filling:
    - `assets/consistency_template.md`
  - Ensure all outputs are saved under:
    - `outputs/` (within the skill directory)

- **Granularity and actionability**
  - Record discrepancies at the most specific level possible (e.g., Figure 2B vs Figure 2 overall).
  - Provide a concrete **Suggested Revision** whenever feasible (e.g., align terminology, correct numbers/units, add missing reference).

- **Language**
  - Default output language is **Chinese**.
  - If the user explicitly specifies another language, output in that language.

## 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

| Field | Required | Format/Source | Example | If Missing |
|---|---|---|---|---|
| User task description | Yes | Text | Research question, writing goal, analysis objective | Stop and ask user to provide |
| Primary input material | Depends on task | Text, file path, ID, table, or literature | PMID, PDF, CSV, DOCX, keywords, etc. | Specify which material type is missing |
| Output preference | No | Text | Language, format, target journal, template | Use 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.


## Input Validation

This skill accepts requests that match the documented purpose of `result-figure-consistencycheck` 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:

> `result-figure-consistencycheck` only handles its documented workflow. Please provide the missing required inputs or switch to a more suitable skill.

## 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.