I2b2-etl: Python application for importing electronic health data into the informatics for integrating biology and the bedside platform

MOTIVATION: The i2b2 platform is used at major academic health institutions and research consortia for querying for electronic health data. However, a major obstacle for wider utilization of the platform is the complexity of data loading that entails a steep curve of learning the platform’s complex data schemas. To address this problem, we have developed the i2b2-etl package that simplifies the data loading process, which will facilitate wider deployment and utilization of the platform. RESULTS: We have implemented i2b2-etl as a Python application that imports ontology and patient data using simplified input file schemas and provides inbuilt record number de-identification and data validation. We describe a real-world deployment of i2b2-etl for a population-management initiative at MassGeneral Brigham. AVAILABILITY AND IMPLEMENTATION: i2b2-etl is a free, open-source application implemented in Python available under the Mozilla 2 license. The application can be downloaded as compiled docker images. A live demo is available at https://i2b2clinical.org/demo-i2b2etl/ (username: demo, password: Etl@2021). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.