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

Pick the report family and load its detailed reference (see index below).
Draft from the template in assets/ for that report type.
Apply regulatory controls — de-identify, document consent, meet timelines.
Validate with the matching scripts/ validator before sign-out.
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.