Medical-research-skills clinical-reports

Source: https://github.com/aipoch/medical-research-skills

When to Use

Use this skill when you need to:

1. Draft a journal-ready clinical case report that follows CARE guidelines and includes consent/de-identification.
2. Produce diagnostic reports (radiology, pathology, laboratory) that are structured, actionable, and consistent with common standards (e.g., ACR/CAP conventions).
3. Prepare clinical trial safety documentation, especially Serious Adverse Event (SAE) narratives and submissions under regulatory timelines.
4. Write an ICH E3–aligned Clinical Study Report (CSR) for sponsor/regulatory submission, including appendices and traceable data presentation.
5. Create or QA patient medical record documentation (SOAP notes, H&P, discharge summaries) for continuity of care, billing support, and medico-legal defensibility.

Key Features

• Template-driven authoring for:
  • Case reports (CARE)
  • Radiology / pathology / lab reports
  • SAE reports and CSR (ICH E3)
  • SOAP, H&P, discharge summaries
• Compliance-first workflow
  • HIPAA de-identification (Safe Harbor identifiers checklist)
  • FDA documentation awareness (e.g., 21 CFR Parts 11/50/56/312)
  • ICH-GCP principles (data integrity, auditability, consent, protocol adherence)
• Validation and QA tooling
  • Completeness checks per report type
  • De-identification scanning
  • Consistency checks across sections (dates, identifiers, outcomes)
• Publication-quality data presentation guidance
  • Tables/figures conventions, labeling, precision, and safety summaries
  • Trial flow diagrams and case timelines
• Reference and asset library integration
  • Uses supporting files under

    references/

    and

    assets/

    for standards and templates

Dependencies

• Python 3.10+
• (Optional, for automation scripts) Common Python tooling typically used in this repository:

  • argparse

    (stdlib)

  • re

    (stdlib)

  • json

    (stdlib)

Note: The provided scripts and templates are referenced by path (e.g.,

scripts/validate_case_report.py

). If your repository defines additional pinned packages (e.g., in

requirements.txt

), use those versions as the source of truth.

Example Usage

Below is a complete, runnable example that generates a report skeleton, validates it, and checks de-identification. Adjust paths to match your repository layout.

1) Generate a template (interactive or parameterized)

python scripts/generate_report_template.py

If the generator supports arguments in your repo, you can typically do something like:

python scripts/generate_report_template.py --type case-report --out reports/case_report.md

2) Validate a CARE case report draft

python scripts/validate_case_report.py reports/case_report.md

3) Check HIPAA de-identification (Safe Harbor scan)

python scripts/check_deidentification.py reports/case_report.md

4) (Optional) Validate a clinical trial report structure (ICH E3)

python scripts/validate_trial_report.py reports/csr.md

5) Use a template asset directly (copy and fill)

cp assets/soap_note_template.md reports/soap_note.md

Recommended supporting references while writing:

• CARE and case report guidance:

  references/case_report_guidelines.md

• Diagnostic reporting standards:

  references/diagnostic_reports_standards.md

• Trial reporting (SAE/CSR, ICH E3):

  references/clinical_trial_reporting.md

• Regulatory compliance (HIPAA/FDA/ICH-GCP):

  references/regulatory_compliance.md

Implementation Details

1) Report Types and Required Sections (High-Level)

Case reports (CARE-aligned) typically require:

• Title/keywords/abstract
• Patient information (de-identified) + consent statement
• Clinical findings + timeline
• Diagnostic assessment (tests + differential + rationale)
• Therapeutic interventions (dose/route/duration + rationale)
• Follow-up/outcomes (including PROs when available)
• Discussion (novelty, literature context, limitations, implications)

Reference:

references/case_report_guidelines.md

Radiology reports commonly follow:

• Indication → technique → comparison → findings → impression (with recommendations)
• Prefer standardized lexicons and structured reporting where applicable (e.g., BI-RADS, LI-RADS)

Reference:

references/diagnostic_reports_standards.md

Pathology reports commonly follow:

• Specimen/clinical history → gross → microscopic → diagnosis (synoptic elements for cancer) → comment
• CAP-style synoptic checklists improve completeness for oncology

Reference:

references/diagnostic_reports_standards.md

Laboratory reports commonly include:

• Patient/specimen metadata → method → results (units + reference ranges) → interpretation (if applicable)
• Critical value handling requires documented notification workflow

Reference:

references/diagnostic_reports_standards.md

SAE reports should capture:

• Seriousness criteria, severity, outcome
• Causality + expectedness with rationale
• Action taken, concomitant therapy, and a coherent narrative timeline
• Regulatory timelines (e.g., 7/15-day rules depending on jurisdiction and event type)

Reference:

references/clinical_trial_reporting.md

CSR (ICH E3) should be:

• Traceable to protocol/SAP, transparent about deviations, and complete in safety/efficacy presentation
• Structured per ICH E3 sections with appendices (protocol, amendments, sample CRFs, listings)

Reference:

assets/clinical_trial_csr_template.md

,

references/clinical_trial_reporting.md

2) HIPAA De-identification (Safe Harbor)

De-identification checks should ensure removal/modification of the 18 HIPAA identifiers, including:

• Names, detailed geography, full dates (except year), contact info, MRNs, account numbers, device identifiers, URLs/IPs, biometrics, full-face photos, and other unique identifiers.

Operational guidance:

• Prefer relative time (“3 months prior”) or year-only when feasible.
• Avoid institution names unless essential and permitted.
• Ensure images are cropped/blurred and consented if potentially identifying.

Reference:

references/regulatory_compliance.md

3) Quality Validation Logic (What the scripts should enforce)

Typical validation checks implemented by repository scripts (by intent) include:

• Completeness: required headings/fields exist for the chosen report type.
• Internal consistency: dates, subject IDs, outcomes, and interventions do not conflict across sections.
• Terminology hygiene: discourages unsafe abbreviations (e.g., Joint Commission “Do Not Use” list) and encourages standard nomenclatures (SNOMED CT, LOINC, ICD-10-CM, CPT) when coding is required.
• Regulatory readiness: presence of consent statements (when applicable), GCP/ethics statements for trials, and documentation of deviations/CAPA where relevant.

References:

• Terminology:

  references/medical_terminology.md

• Data presentation:

  references/data_presentation.md

• QA checklists:

  assets/quality_checklist.md

  ,

  assets/hipaa_compliance_checklist.md

4) Recommended Assets and Scripts (Repository Paths)

Templates (

assets/

)

• assets/case_report_template.md

• assets/radiology_report_template.md

• assets/pathology_report_template.md

• assets/lab_report_template.md

• assets/clinical_trial_sae_template.md

• assets/clinical_trial_csr_template.md

• assets/soap_note_template.md

• assets/history_physical_template.md

• assets/discharge_summary_template.md

Automation (

scripts/

)

• scripts/validate_case_report.py

• scripts/validate_trial_report.py

• scripts/check_deidentification.py

• scripts/compliance_checker.py

• scripts/terminology_validator.py

Use these to standardize structure, reduce omissions, and improve compliance before submission or chart finalization.