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

Abstract

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 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.