Development of Data Ingestion Pipelines for the Federated Use of Biomedical Data in Research: The Health Big Data Project

The secondary use of health data represents a great opportunity to advance pathophysiological knowledge and improve patients’ care. However, the absence of standard data formats and information structuring schemas severely hinders this potential, preventing the efficient sharing of data collected in different hospitals and affecting the quality of multicentric studies. The 10-year Health Big Data (HBD) project aims to address these issues to foster the collaboration of 51 Italian research hospitals (IRCCSs). To address the seven main challenges identified for health data sharing, seven Working Groups (WGs) were created, with the WG2 being responsible for the definition of standardization and harmonization pipelines for signals, bioimages, and omics data. The present paper focuses on two ongoing works of the WG2, namely the implementation of a pipeline to extract and map information from electrocardiographic (ECG) signals into the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) and the development of a harmonization pipeline to reduce the center effect in multicentric Magnetic Resonance Imaging (MRI) studies. We show interesting results and insights concerning the implementation of both pipelines. Besides, we highlight the main difficulties we encountered on our path toward health data sharing and suggest possible solutions.