clinical-reports

Clinical Reports Skill

Overview

Comprehensive skill for writing clinical reports including case reports, diagnostic reports, clinical trial reports, and patient documentation. Provides full support with templates, regulatory compliance, and validation tools.

What's Included

📋 Four Major Report Types

1. Clinical Case Reports - CARE-compliant case reports for medical journal publication
2. Diagnostic Reports - Radiology (ACR), pathology (CAP), and laboratory reports
3. Clinical Trial Reports - SAE reports, Clinical Study Reports (ICH-E3), DSMB reports
4. Patient Documentation - SOAP notes, H&P, discharge summaries, consultation notes

📚 Reference Files (8 comprehensive guides)

• case_report_guidelines.md - CARE guidelines, de-identification, journal requirements
• diagnostic_reports_standards.md - ACR, CAP, CLSI standards, structured reporting systems
• clinical_trial_reporting.md - ICH-E3, CONSORT, SAE reporting, MedDRA coding
• patient_documentation.md - SOAP notes, H&P, discharge summary standards
• regulatory_compliance.md - HIPAA, 21 CFR Part 11, ICH-GCP, FDA regulations
• medical_terminology.md - SNOMED-CT, LOINC, ICD-10, CPT codes
• data_presentation.md - Clinical tables, figures, Kaplan-Meier curves
• peer_review_standards.md - Review criteria for clinical manuscripts

📄 Templates (12 professional templates)

• case_report_template.md - Structured case report following CARE guidelines
• soap_note_template.md - SOAP progress note format
• history_physical_template.md - Complete H&P examination template
• discharge_summary_template.md - Hospital discharge documentation
• consult_note_template.md - Specialist consultation format
• radiology_report_template.md - Imaging report with structured reporting
• pathology_report_template.md - Surgical pathology with CAP synoptic elements
• lab_report_template.md - Clinical laboratory test results
• clinical_trial_sae_template.md - Serious adverse event report form
• clinical_trial_csr_template.md - Clinical study report outline (ICH-E3)
• quality_checklist.md - Quality assurance for all report types
• hipaa_compliance_checklist.md - Privacy and de-identification verification

🔧 Validation Scripts (8 automation tools)

• validate_case_report.py - Check CARE guideline compliance and completeness
• check_deidentification.py - Scan for 18 HIPAA identifiers in reports
• validate_trial_report.py - Verify ICH-E3 structure and required elements
• format_adverse_events.py - Generate AE summary tables from CSV data
• generate_report_template.py - Interactive template selection and generation
• extract_clinical_data.py - Parse and extract structured clinical data
• compliance_checker.py - Verify regulatory compliance requirements
• terminology_validator.py - Validate medical terminology and prohibited abbreviations

Quick Start

Generate a Template

cd .claude/skills/clinical-reports/scripts
python generate_report_template.py

# Or specify type directly
python generate_report_template.py --type case_report --output my_case_report.md

Validate a Case Report

python validate_case_report.py my_case_report.md

Check De-identification

python check_deidentification.py my_case_report.md

Validate Clinical Trial Report

python validate_trial_report.py my_csr.md

Key Features

CARE Guidelines Compliance

• Complete CARE checklist coverage
• De-identification verification
• Informed consent documentation
• Timeline creation assistance
• Literature review integration

Regulatory Compliance

• HIPAA - Privacy protection, 18 identifier removal, Safe Harbor method
• FDA - 21 CFR Parts 11, 50, 56, 312 compliance
• ICH-GCP - Good Clinical Practice standards
• ALCOA-CCEA - Data integrity principles

Professional Standards

• ACR - American College of Radiology reporting standards
• CAP - College of American Pathologists synoptic reporting
• CLSI - Clinical Laboratory Standards Institute
• CONSORT - Clinical trial reporting
• ICH-E3 - Clinical study report structure

Medical Coding Systems

• ICD-10-CM - Diagnosis coding
• CPT - Procedure coding
• SNOMED-CT - Clinical terminology
• LOINC - Laboratory observation codes
• MedDRA - Medical dictionary for regulatory activities

Common Use Cases

1. Publishing a Clinical Case Report

> Create a clinical case report for a 65-year-old patient with atypical 
  presentation of acute appendicitis

> Check this case report for HIPAA compliance
> Validate against CARE guidelines

2. Writing Diagnostic Reports

> Generate a radiology report template for chest CT
> Create a pathology report for colon resection specimen with adenocarcinoma
> Write a laboratory report for complete blood count

3. Clinical Trial Documentation

> Write a serious adverse event report for hospitalization due to pneumonia
> Create a clinical study report outline for phase 3 diabetes trial
> Generate adverse events summary table from trial data

4. Patient Clinical Notes

> Create a SOAP note for follow-up visit
> Generate an H&P for patient admitted with chest pain
> Write a discharge summary for heart failure hospitalization
> Create a cardiology consultation note

Workflow Examples

Case Report Workflow

1. Obtain informed consent from patient
2. Generate template: python generate_report_template.py --type case_report
3. Write case report following CARE structure
4. Validate compliance: python validate_case_report.py case_report.md
5. Check de-identification: python check_deidentification.py case_report.md
6. Submit to journal with CARE checklist

Clinical Trial SAE Workflow

1. Generate SAE template: python generate_report_template.py --type sae
2. Complete SAE form within 24 hours of event
3. Assess causality using WHO-UMC or Naranjo criteria
4. Validate completeness: python validate_trial_report.py sae_report.md
5. Submit to sponsor within regulatory timelines (7 or 15 days)
6. Notify IRB per institutional policy

Best Practices

Privacy and Ethics

✓ Always obtain informed consent for case reports
✓ Remove all 18 HIPAA identifiers before publication
✓ Use de-identification validation scripts
✓ Document consent in manuscript
✓ Consider re-identification risk for rare conditions

Clinical Quality

✓ Use professional medical terminology
✓ Follow structured reporting templates
✓ Include all required elements
✓ Document chronology clearly
✓ Support diagnoses with evidence

Regulatory Compliance

✓ Meet SAE reporting timelines (7-day, 15-day)
✓ Follow ICH-E3 structure for CSRs
✓ Maintain ALCOA-CCEA data integrity
✓ Document protocol adherence
✓ Use MedDRA coding for adverse events

Documentation Standards

✓ Sign and date all clinical notes
✓ Document medical necessity
✓ Use standard abbreviations only
✓ Avoid prohibited abbreviations (JCAHO "Do Not Use" list)
✓ Maintain legibility and completeness

Integration

The clinical-reports skill integrates seamlessly with:

• scientific-writing - For clear, professional medical writing
• peer-review - For quality assessment of case reports
• citation-management - For literature references in case reports
• research-grants - For clinical trial protocol development

Resources

External Standards

• CARE Guidelines: https://www.care-statement.org/
• ICH-E3 Guideline: https://database.ich.org/sites/default/files/E3_Guideline.pdf
• CONSORT Statement: http://www.consort-statement.org/
• HIPAA: https://www.hhs.gov/hipaa/
• ACR Practice Parameters: https://www.acr.org/Clinical-Resources/Practice-Parameters-and-Technical-Standards
• CAP Cancer Protocols: https://www.cap.org/protocols-and-guidelines

Professional Organizations

• American Medical Association (AMA)
• American College of Radiology (ACR)
• College of American Pathologists (CAP)
• Clinical Laboratory Standards Institute (CLSI)
• International Council for Harmonisation (ICH)

Support

For issues or questions about the clinical-reports skill:

1. Check the comprehensive reference files
2. Review templates for examples
3. Run validation scripts to identify issues
4. Consult the SKILL.md for detailed guidance

License

Part of the Claude Scientific Writer project. See main LICENSE file.