Alterlab Clinical Reports

---
name: alterlab-clinical-reports
description: Writes comprehensive clinical reports — case reports (CARE guidelines), diagnostic reports (radiology, pathology, lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP notes, H&P, discharge summaries) — with templates, regulatory compliance (HIPAA, FDA, ICH-GCP), and validation tools. Use when drafting a case report for journal publication, a radiology/pathology/lab diagnostic report, an ICH-E3 clinical study report (CSR) or SAE narrative, or SOAP/H&P/discharge patient records needing regulatory-compliant formatting. Part of the AlterLab Academic Skills suite.
allowed-tools: Read Write Edit Bash
license: MIT
compatibility: "Runs with Read/Write/Edit/Bash; producing PDF/report output requires a local LaTeX toolchain. No API key required."
metadata:
    skill-author: AlterLab
    version: "1.1.0"
    last_updated: "2026-09-23"
---

# Clinical Report Writing

## Overview

Document medical information with precision, accuracy, and regulatory compliance.
This skill covers four report families: **case reports** for journal publication,
**diagnostic reports** for clinical practice (radiology, pathology, lab),
**clinical trial reports** for regulatory submission (SAE, CSR), and **patient
documentation** for medical records (SOAP, H&P, discharge).

Clinical reports have to be accurate, complete, objective, and compliant with the
applicable regulations (HIPAA, FDA, ICH-GCP), because they feed patient care, regulatory
decisions, and the published record. Use only clinical data the user provides — never
invent findings, lab values, dates, or citations to fill a template — and mark anything
unknown as a placeholder for the clinician to complete. Drafts are for review and
sign-off by the responsible clinician or investigator.

## When to Use This Skill

Use when:
- Writing a clinical case report for journal submission (CARE guidelines)
- Creating a diagnostic report (radiology, pathology, laboratory)
- Documenting clinical trial data, SAE narratives, or a CSR (ICH-E3)
- Writing SOAP notes, H&P, discharge summaries, or consult notes
- Ensuring HIPAA compliance and proper de-identification
- Validating clinical documentation for completeness and accuracy

### Does NOT Trigger

| Scenario | Use Instead |
|----------|-------------|
| Group-level cohort analysis or GRADE-graded treatment recommendations | `alterlab-clinical-decision` |
| A forward-looking care plan with SMART goals for one patient | `alterlab-treatment-plans` |
| Designing CRFs/REDCap instruments or mapping trial data to CDISC SDTM | `alterlab-redcap-cdisc` |
| An IMRaD research manuscript (e.g. an RCT results paper) rather than a case report or CSR | `alterlab-scientific-writing` |
| IRB applications and informed-consent forms | `alterlab-research-ethics` |

## Core Workflow

1. **Pick the report family** and load its detailed reference (see index below).
2. **Draft from the template** in `assets/` for that report type.
3. **Apply regulatory controls** — de-identify, document consent, meet timelines.
4. **Validate** with the matching `scripts/` validator before sign-out.
5. **Final QA** against the checklist at the end of this file.

### 1. Case reports for journal publication
Follow the CARE (CAse REport) checklist: title, keywords, structured abstract,
introduction, patient information, clinical findings, timeline, diagnostic
assessment, therapeutic interventions, follow-up/outcomes, discussion, patient
perspective, and informed consent. Mind journal-specific limits (word count,
figures, reference style) and de-identify before submission.
→ Element-by-element detail, journal requirements, and the 18 HIPAA identifiers:
`references/care_report_sections.md`. High-level checklist: `references/case_report_guidelines.md`.

### 2. Diagnostic reports (radiology, pathology, laboratory)
Each uses a standardized section structure (demographics → indication → technique →
comparison → findings → impression for radiology; gross/microscopic/diagnosis for
pathology; results with reference ranges and critical-value reporting for lab).
Use structured-reporting templates (BI-RADS, Lung-RADS, CAP synoptic) where they apply.
→ Full section templates: `references/diagnostic_report_templates.md`.
Standards and lexicons (ACR, CAP, LOINC): `references/diagnostic_reports_standards.md`.

### 3. Clinical trial reports (SAE, CSR, deviations)
SAE reports document serious adverse events with causality and expectedness, on
strict regulatory timelines (7/15 days). CSRs follow the ICH-E3 section structure
for regulatory submission. Protocol deviations are categorized (minor/major/violation)
with CAPA documentation. Journal reports of randomized trials follow CONSORT 2025
(30-item checklist, April 2025; replaces CONSORT 2010), and trial protocols follow
SPIRIT 2025.
→ Component-by-component structures: `references/clinical_trial_report_structures.md`.
Regulatory framing (ICH-E3, CONSORT, timelines): `references/clinical_trial_reporting.md`.

### 4. Patient documentation (SOAP, H&P, discharge)
SOAP notes for progress, H&P for admission/initial encounters, discharge summaries
for handoff to outpatient providers. Use standard abbreviations, sign and date,
document medical necessity for billing.
→ Format structures: `references/patient_record_formats.md`.
Coding and documentation guidance: `references/patient_documentation.md`.

## Regulatory Compliance and Privacy

- **HIPAA**: minimum-necessary disclosure; de-identify via Safe Harbor (remove 18
  identifiers) or Expert Determination; Business Associate Agreements for third parties.
- **FDA**: 21 CFR Part 11 (e-records/signatures), Part 50 (consent), Part 56 (IRB),
  Part 312 (IND).
- **ICH-GCP**: E6(R3) (ICH Step 4, 6 January 2025; in effect in the EU since 23 July
  2025) — protocol adherence, consent documentation, source-document requirements,
  audit trails, investigator responsibilities. Check which revision applied when a
  given study was conducted.

> **⚠️ Caveat — automated de-identification is NOT a compliance guarantee.** The bundled `scripts/check_deidentification.py` is a *pure regex* scan. Pattern matching has known, substantial false-negative rates: it misses unconventional name spellings, free-text dates, narrative addresses, rare identifiers, and anything outside its fixed patterns. It is a rough first-pass screen only — **not** a substitute for line-by-line manual review by a qualified person, and **not** a validated de-identification tool (e.g., Microsoft Presidio, Philter, or a certified Expert Determination). Passing this script does not establish HIPAA Safe Harbor compliance and must never be relied upon as a privacy guarantee. Always perform manual review before any disclosure or publication.

Detailed guidance: `references/regulatory_compliance.md`.

## Medical Terminology and Standards

Use standardized nomenclature: **SNOMED CT** (clinical terms), **LOINC** (lab/clinical
observations), **ICD-10-CM** (diagnosis coding), **CPT** (procedure coding). Respect the
Joint Commission "Do Not Use" abbreviation list (e.g. write "unit" not "U", always use a
leading zero, never a trailing zero).
Comprehensive standards: `references/medical_terminology.md`.

## Data Presentation

Tables for demographics, adverse events, lab values over time, and efficacy outcomes;
figures for Kaplan-Meier curves, forest plots, CONSORT flow diagrams, and case-report
timelines. Images must be ≥300 dpi, de-identified, with consent for recognizable
patients. Detail: `references/data_presentation.md`.

## Quality Assurance

Documentation must be **complete, accurate, timely, clear, and compliant**. Use the
per-type validation checklists (CARE, diagnostic completeness, SAE regulatory
compliance, billing requirements) and the `scripts/` validators.

## Workflows by Report Type

- **Case report**: identify case + consent → literature review → draft (CARE) → internal
  review → journal selection/submission → revision.
- **Diagnostic report**: review indication/priors → interpret → dictate structured report
  → peer review (complex cases) → sign-out → critical-value notification. STAT <1h,
  routine 24-48h.
- **SAE report**: identify → assess/document → causality + expectedness → review →
  submit to sponsor/IRB/FDA → follow-up to resolution (24h-15 days).
- **CSR**: database lock → analysis per SAP → medical-writer draft → biostat/clinical
  review → QC → approval/submission (6-12 months post-completion).

## Index of Bundled Resources

### References (`references/`)
- `care_report_sections.md` — CARE element-by-element, journal requirements, 18 HIPAA identifiers
- `case_report_guidelines.md` — CARE guidelines, journal requirements, writing tips
- `diagnostic_report_templates.md` — radiology/pathology/lab section templates
- `diagnostic_reports_standards.md` — ACR, CAP, laboratory reporting standards
- `clinical_trial_report_structures.md` — SAE/CSR/deviation component structures
- `clinical_trial_reporting.md` — ICH-E3, CONSORT, SAE reporting, CSR structure
- `patient_record_formats.md` — SOAP/H&P/discharge section formats
- `patient_documentation.md` — SOAP, H&P, discharge, coding
- `regulatory_compliance.md` — HIPAA, 21 CFR Part 11, ICH-GCP, FDA
- `medical_terminology.md` — SNOMED, LOINC, ICD-10, abbreviations
- `data_presentation.md` — tables, figures, safety data, CONSORT diagrams
- `peer_review_standards.md` — review criteria for clinical manuscripts

### Template assets (`assets/`)
`case_report_template.md`, `radiology_report_template.md`, `pathology_report_template.md`,
`lab_report_template.md`, `clinical_trial_sae_template.md`, `clinical_trial_csr_template.md`,
`soap_note_template.md`, `history_physical_template.md`, `discharge_summary_template.md`,
`consult_note_template.md`, `quality_checklist.md`, `hipaa_compliance_checklist.md`.

### Automation scripts (`scripts/`)
`validate_case_report.py`, `validate_trial_report.py`, `check_deidentification.py`,
`format_adverse_events.py`, `generate_report_template.py`, `extract_clinical_data.py`,
`compliance_checker.py`, `terminology_validator.py`.

## Integration with Other Skills

Pairs with `alterlab-scientific-writing` (clear medical prose), `alterlab-peer-review`
(quality assessment), `alterlab-citation-mgmt` (literature references),
`alterlab-research-grants` (protocol development), and `alterlab-literature-review`
(background sections).

## Common Pitfalls

- **Case reports**: privacy violations, lack of novelty, insufficient detail, weak
  literature review, overgeneralization from a single case.
- **Diagnostic reports**: vague language, incomplete comparison, missing clinical
  correlation, delayed critical-value notification.
- **Trial reports**: late SAE reporting, incomplete causality, data inconsistencies,
  unreported deviations, selective reporting.
- **Patient documentation**: copy-forward errors, insufficient detail affecting billing,
  missing medical necessity, unsigned/undated notes.

## Final Checklist

Before finalizing any clinical report, verify:

- [ ] All required sections complete
- [ ] Patient privacy protected (HIPAA compliance)
- [ ] Informed consent obtained (if applicable)
- [ ] Accurate and verified clinical data
- [ ] Appropriate medical terminology and coding
- [ ] Clear, professional language
- [ ] Proper formatting per guidelines
- [ ] References cited appropriately
- [ ] Figures and tables labeled correctly
- [ ] Spell-checked and proofread
- [ ] Regulatory requirements met
- [ ] Institutional policies followed
- [ ] Signatures and dates present
- [ ] Quality assurance review completed

Clinical report quality directly affects patient safety, healthcare delivery, and the
medical literature, so accuracy and privacy take precedence over polish.

Part of the AlterLab Academic Skills suite.