From Routine Healthcare Data to Research-Ready Cohorts: A Structured Preprocessing Framework

Routine clinical data offer significant potential for data-driven research and real-world evidence. However, such data are typically heterogeneous, irregular, and not designed for research use. This has a detrimental effect on the transformation of the data into analysis-ready datasets. The following paper sets out a preprocessing framework that converts routine clinical data into research-ready datasets. The approach was developed in the context of a use case concerning kidney transplant rejection diagnostics, with the objective of reconstructing clinically meaningful treatment trajectories. The proposed framework is comprised of three distinct steps: firstly, recursive event classification (rEC), then context-sensitive event annotation (cEA), and finally, context-based time series harmonisation (cTSH). The purpose of the framework is to transform irregular measurements into standardised temporal representations. When applied to routine data, the framework generated structured, comparable datasets that resemble clinical study data. These enable statistical modelling, machine learning, and systematic data reuse.