Challenges and Recommendations for Electronic Health Records Data Extraction and Preparation for Dynamic Prediction Modeling in Hospitalized Patients: Practical Guide and Tutorial
Elena Simona Albu, Shan Gao, Pieter Stijnen, Frank E Rademakers, Bas C. T. van Bussel, Taya Annabelle Collyer, Tina Hernandez‐Boussard, Laure Wynants, Ben Van Calster · Journal of Medical Internet Research · 2025
Dynamic predictive modeling using electronic health record data has gained significant attention in recent years. The reliability and trustworthiness of such models depend heavily on the quality of the underlying data, which is, in part, determined by the stages preceding the model development: data extraction from electronic health record systems and data preparation. In this paper, we identified over 40 challenges encountered during these stages and provided actionable recommendations for addressing them. These challenges are organized into 4 categories: cohort definition, outcome definition, feature engineering, and data cleaning. This comprehensive list serves as a practical guide for data extraction engineers and researchers, promoting best practices and improving the quality and real-world applicability of dynamic prediction models in clinical settings.