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

AI Article Synopsis

Article 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 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.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9563689PMC
http://dx.doi.org/10.1093/bioinformatics/btac595DOI Listing

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