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":"1.0.0"}

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).

Critical principle: clinical reports must be accurate, complete, objective, and compliant with applicable regulations (HIPAA, FDA, ICH-GCP). Patient privacy and data integrity are paramount.

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

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. → 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: protocol adherence, consent documentation, source-document requirements, audit trails, investigator responsibilities.

⚠️ 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 scientific-writing (clear medical prose), peer-review (quality assessment), citation-mgmt (literature references), research-grants (protocol development), and 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

Final note: clinical report quality directly impacts patient safety, healthcare delivery, and medical knowledge. Always prioritize accuracy, privacy, and professionalism.