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scientific_writer/.claude/skills/clinical-reports/README.md

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+# 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
+
+```bash
+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
+
+```bash
+python validate_case_report.py my_case_report.md
+```
+
+### Check De-identification
+
+```bash
+python check_deidentification.py my_case_report.md
+```
+
+### Validate Clinical Trial Report
+
+```bash
+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.
+