Towards FAIR Clinical Registries: A Privacy-by-Design Framework for Migrating Legacy Document-Based Clinical Reports...

Clinical registries are vital for research, yet many documents and reports still only exist as legacy Word documents or PDFs, making data reuse and interoperability difficult. Manual data entry into modern systems is slow and error-prone, and migration is further complicated by privacy regulations and restricted hospital networks. We developed a privacy-by-design pipeline that automatically converts document-based right-heart-catheterization (RHC) reports into structured, research-ready data in REDCap. The workflow uses deterministic parsing and domain-specific mapping, enforces longitudinal consistency across repeated examinations, and includes a mandatory anonymisation checkpoint before any data leaves the clinical domain. Deployed for a growing pulmonary hypertension registry (>5000 patients), the system produces auditable, reproducible outputs and substantially reduces manual effort while maintaining GDPR compliance. This approach offers a practical path to modernizing document-based registries and advancing FAIR-aligned, scalable research infrastructures.