Clinical Report Writing

Overview

Write comprehensive clinical reports including 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). Includes regulatory compliance and validation tools.

Getting Started

Add your source materials to the project workspace, then activate the Clinical Report Writing skill. The agent will guide you through the process step by step.

Example Conversation

You: I need a case report for journal submission following CARE guidelines. I’ve added my notes and the patient timeline (de-identified).
Agent: I’ll draft a CARE-compliant case report. I’ve read your notes and timeline. A few clarifications: (1) What is the main clinical lesson or novelty you want the conclusion to stress? (2) Do you have consent for publication and have all 18 HIPAA identifiers been removed or generalised?
You: The lesson is early imaging changed management. Yes, consent on file and I’ve stripped identifiers — can you double-check with the de-ID script?
Agent: I’ve run the de-identification checker; one date pattern was flagged (admission date in the timeline). I’ve generalised it to “Day 0” in the draft. I’ve created output/case-report-draft.md with CARE sections: title, keywords, abstract, introduction, patient information, clinical findings, timeline, diagnostic assessment, therapeutic interventions, follow-up, and discussion. I also ran the CARE validator — all required elements are present. Want to add a figure (e.g. timeline or algorithm) or refine the discussion?

Sample Output Excerpt

Below is a representative excerpt from a clinical case report (CARE structure).

Abstract

Introduction: Unusual presentation of [condition] in [population] is rarely reported; early recognition improves outcomes.

Patient concerns: A [age]-year-old [sex] presented with [chief complaint] and [key history].

Diagnoses: [Primary diagnosis] with [differential/contributing factors].

Interventions: [Key treatments and procedures].

Outcomes: [Clinical outcome and follow-up duration].

Conclusions: This case highlights the importance of [clinical lesson]. Early [diagnostic/therapeutic] intervention may alter course.

Timeline (excerpt)

Day	Event
0	Presentation; [key findings].
1	[Test] performed; [result].
3	[Treatment] initiated.
7	Improvement in [metric].
30	Follow-up; [outcome].

Built-in Scripts and Validation

The skill includes several scripts to support quality, compliance, and consistency. The agent can run them during or after drafting.

Validation scripts

Script	Purpose
validate_case_report.py	Checks case reports against the CARE (CAse REport) guidelines: title, keywords, abstract, introduction, patient information, clinical findings, timeline, diagnostic assessment, therapeutic interventions, follow-up, discussion. Reports required vs. present and any missing elements.
validate_trial_report.py	Validates Clinical Study Reports (CSR) against ICH-E3 structure: title page, synopsis, TOC, abbreviations, ethics, investigators, introduction, objectives, study patients, efficacy, safety, discussion, tables/figures, references, appendices. Returns a compliance rate and section-level pass/fail.
check_deidentification.py	Scans text for the 18 HIPAA identifiers (e.g. names, geographic data smaller than state, dates except year, telephone, SSN, MRN, device IDs). Flags potential privacy violations with severity so you can remove or generalise before publication or sharing.
compliance_checker.py	Checks for regulatory compliance patterns: HIPAA (consent, de-identification), GCP (IRB/ethics approval, protocol, informed consent), FDA (study/IDE/IND identifiers, safety/adverse event reporting). Useful as a quick pass before submission.
terminology_validator.py	Validates medical terminology: JCAHO “Do Not Use” abbreviations (e.g. U, IU, QD, MS, MSO4, MgSO4) with suggested replacements; flags ambiguous abbreviations (e.g. cc, hs, SC, D/C); and reports ICD-10-style codes found in the text.

Utility scripts

Script	Purpose
generate_report_template.py	Interactive template generator: lists available clinical report templates (case report, CSR, SOAP, discharge summary, etc.) and generates a starter file with the chosen structure.
format_adverse_events.py	Converts CSV or structured adverse event data into formatted AE summary tables suitable for inclusion in clinical trial reports.
extract_clinical_data.py	Extracts structured clinical data from reports (e.g. vital signs, demographics, medications) for consistency checks or data tables.

The agent runs validators when appropriate (e.g. CARE after drafting a case report, de-identification before finalising) and surfaces findings so you can fix gaps iteratively.