Write Protocol

Write-Protocol Skill

Draft the scientific core of an IRB/ethics protocol and leave institution-specific sections as [TODO] skeletons. Read both reference files before generating a protocol draft:

• ${CLAUDE_SKILL_DIR}/references/protocol_template.md -- the 10-section structure, per-section guidance, and the [TODO] blocks for Sections 5-9
• ${CLAUDE_SKILL_DIR}/references/ethics_checklist.md -- jurisdiction-specific ethical requirements

Inputs

Collect the required inputs before generating; ask for any that are missing.

• Required: research question / hypothesis (specific, testable); study type (retrospective cohort, prospective cohort, cross-sectional, RCT, diagnostic accuracy, case-control, case series); target population (who, where, when); primary outcome; secondary outcomes (if any).
• Optional: key references (DOIs or search terms); institution name (header and ethics guidance); regulatory context -- Korea (PIPA), US (HIPAA/Common Rule), EU (GDPR), other.

Use prior skill outputs directly when they exist; when they do not, ask the user or call the skill:

• design-study: design recommendations, analysis unit, comparator design, validation strategy.
• calc-sample-size: protocol/sample_size_justification.md (canonical IRB-ready prose) and protocol/sample_size_calc.{R,py} (reproducible code).
• search-lit: Background references with verified citations.
• define-variables: variable_operationalization.md -- literature-grounded definitions, cutoffs, DB-variable mappings for the Methods section. Precondition: if the study is observational and no operationalization artifact exists, call /define-variables before drafting Methods. Do not invent phenotype/cutoff definitions from the data dictionary inside this skill.

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Protocol Structure -- 10 Sections

Core Sections (Fully Generated)

Section 1: Background and Rationale (400-600 words)

Full paragraphs, no bullet points, flowing from clinical context (disease burden, current practice) through the knowledge gap and rationale (what this study adds) to the research question or hypothesis. Call /search-lit if key references are not provided. Cite a reference only with a /search-lit-confirmed DOI or PMID; otherwise mark it [UNVERIFIED - NEEDS MANUAL CHECK].

Section 2: Study Design and Eligibility Criteria (300-500 words)

Prose covering the study design with its justification (why this design answers this question), the setting (single-center vs multi-center, institution description) and the study period, followed by numbered inclusion and numbered exclusion criteria. If design-study output is available, incorporate its analysis unit (patient vs lesion vs exam), comparator design, validation strategy, and leakage risks with mitigations. Mark any clinical definition, diagnostic criterion or guideline recommendation you cannot confirm [VERIFY] and ask the user.

Section 3: Sample Size Justification (150-300 words)

• If protocol/sample_size_justification.md exists (calc-sample-size output): embed it VERBATIM. Do not rephrase numbers.
• If not available: prompt the user to run /calc-sample-size first; only fall back to a basic justification if the user explicitly declines.
• Must include: test type, expected effect size (with literature source), alpha level, power, attrition adjustment.
• Final statement: "We plan to enroll N participants."

Section 4: Statistical Analysis Plan (300-500 words)

Full prose covering: descriptive statistics (continuous as mean (SD) or median (IQR); categorical as count (%)); the primary analysis (test, assumptions, handling of violations); pre-specified secondary analyses; pre-specified subgroup analyses with interaction tests; missing-data handling (complete case, multiple imputation, sensitivity analysis); software name and version (e.g., R 4.4.0, Python 3.12, SAS 9.4); two-sided alpha = 0.05 unless otherwise justified.