Experiences of Transforming a Complex Nephrologic Care and Research Database into i2b2 Using the IDRT Tools

Journal of Healthcare Engineering
Christian MaierMartin Sedlmayr

Abstract

The secondary use of data from electronic medical records has become an important factor to determine and to identify various causes of disease. For this reason, applications like informatics for integrating biology and the bedside (i2b2) offer a GUI-based front end to select patient cohorts. To make use of those tools, however, clinical data need to be extracted from the Electronic Health Record (EHR) system and integrated into the data schema of i2b2. We used TBase, a documentation system for nephrologic transplantations, as a source system and applied the Integrated Data Repository Toolkit (IDRT) for the Extract, Transform, and Load (ETL) process to load the data into i2b2. Since i2b2 uses an entity-attribute-value (EAV) schema, which is a fundamentally different way of modeling data in comparison to a standard relational schema in TBase, we evaluated if (a) the data relationship of the source system entities can still be represented in the i2b2 schema and if (b) the IDRT is a suitable solution for loading the data of a comprehensive data schema like TBase into i2b2. For that reason, we identified entities in the TBase data schema which were relevant for answering questions on cohort identification. By doing so, we found out...Continue Reading

References

Nov 14, 2006·International Journal of Medical Informatics·Valentin Dinu, Prakash Nadkarni
Aug 22, 2009·Methods of Information in Medicine·Jasmina SucT Ganslandt
Mar 2, 2010·Journal of the American Medical Informatics Association : JAMIA·Shawn N MurphyIsaac Kohane
May 2, 2012·BMC Bioinformatics·Daniele SegagniRiccardo Bellazzi
Oct 26, 2012·BMC Bioinformatics·Riccardo BellazziPaolo Romano
Jan 1, 2011·Applied Clinical Informatics·T GanslandtH U Prokosch
Jan 15, 2015·PloS One·Sebastian MateThomas Ganslandt
Oct 25, 2016·Journal of Biomedical Informatics·Birger HaarbrandtMichael Marschollek
May 13, 2017·International Journal of Medical Informatics·Maria Tereza Fernandes AbrahãoMarco Antonio Gutierrez

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Citations

Mar 30, 2021·Journal of Biomedical Informatics·Yan HuangGuo-Qiang Zhang

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Software Mentioned

Integrated Data Repository Toolkit ( IDRT )
Excel
Talend Open Studio Extract - Load - Transform ELT
IDRT
ONCO
Integrated Data Repository Toolkit ” ( IDRT )
IDRT editor
TBASE
i2b2
Talend Open Studio

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