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

Clinical Study Bias Assessment (QUADAS-2)

This skill evaluates clinical diagnostic accuracy studies for bias and applicability concerns using the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool.

Workflow

To assess a study, follow these steps:

1. Analyze Patient Selection:

   • Assess if the sample was consecutive or random.
   • Check for case-control design (should be avoided).
   • Check for inappropriate exclusions.
   • See references/quadas_2_criteria.md for detailed signaling questions.

2. Analyze Index Test:

   • Assess if the index test results were interpreted without knowledge of the reference standard.
   • Check if the threshold was pre-specified.

3. Analyze Reference Standard:

   • Assess if the reference standard correctly classifies the target condition.
   • Check if reference standard results were interpreted without knowledge of the index test.

4. Analyze Flow and Timing:

   • Assess the interval between index test and reference standard.
   • Check if all patients received the reference standard (and the same one).
   • Check if all patients were included in the analysis.

Output Format

For each domain (Patient Selection, Index Test, Reference Standard, Flow and Timing), you MUST output the findings in the following structure:

### [Domain Name]

**[Signaling Question 1]?**
- Comments: [Explanation in Chinese]
- Quote: [Original text quote]
- Answer: [Yes/No/Unclear]

... (Repeat for all signaling questions)

Quality Rules

1. Language: Explanations (Comments) must be in Chinese.
2. Evidence: Every judgment must be supported by a direct quote from the paper.
3. Strictness: If information is missing, select "Unclear". Do not guess.

PDF Parsing Tool

For processing PDF literature, you can use the provided Python script:

# Install dependencies
pip install PyPDF2

# Extract full text
python scripts/pdf_extractor.py "paper.pdf"

# Extract specific page range
python scripts/pdf_extractor.py "paper.pdf" 5 15

The script will automatically extract the text, which you can then copy and send to me for QUADAS-2 assessment.

Input Validation

This skill accepts requests that match the documented purpose of diagnostic-study-quality-assessment-quadas-2 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:

diagnostic-study-quality-assessment-quadas-2 only handles its documented workflow. Please provide the missing required inputs or switch to a more suitable skill.

References

• QUADAS-2 Criteria: Detailed signaling questions and judgment guidelines.

When to Use

• Use this skill when the user explicitly needs to perform the core task of diagnostic-study-quality-assessment-quadas-2 and has provided the minimum executable input.
• Use this skill when you need a structured deliverable rather than general advice.
• Use this skill when the current task can be completed using this skill's bundled scripts, templates, or reference materials.

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

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.