INTRODUCTION: The secondary use of data in clinical environments offers significant opportunities to enhance medical research and practices. However, extracting data from generic data structures, particularly the Entity-Attribute-Value (EAV) model, remains challenging. This study addresses these challenges by developing a methodological approach to convert EAV-based data into a format more suitable for analysis.

BACKGROUND: The EAV model is widely used in clinical information systems due to its adaptability, but it often complicates data retrieval for research purposes due to its vertical data structure and dynamic schema.

OBJECTIVE: The objective of this study is to develop a methodological approach to address the handling of these generic data structures, Methods: We introduce a five-step methodological approach: 1) understanding the specific clinical processes to determine data collection points and involved roles; 2) analysing the data source to understand the data structure and metadata; 3) reversing a use-case-specific data structure to map the front-end data input to its storage format; 4) analysing the content to identify medical information and establish connections; and 5) managing schema changes to maintain data integrity.

RESULTS: Applying this method to the hospital information system has shown that EAV-based data can be converted into a structured format, suitable for research. This conversion reduced data sparsity and improved the manageability of schema changes without affecting other classes of data.

CONCLUSION: The developed approach provides a systematic method for handling complex data relationships and maintaining data integrity in clinical systems using EAV models. This approach facilitates the secondary use of clinical data, enhancing its utility for medical research and practice.