Combining clinical and genomics queries using i2b2 - Three methods

Shawn N Murphy, Paul Avillach, Riccardo Bellazzi, Lori Phillips, Matteo Gabetta, Alal Eran, Michael T McDuffie, Isaac S. Kohane

Research output: Contribution to journalArticle

Abstract

We are fortunate to be living in an era of twin biomedical data surges: a burgeoning representation of human phenotypes in the medical records of our healthcare systems, and high-throughput sequencing making rapid technological advances. The difficulty representing genomic data and its annotations has almost by itself led to the recognition of a biomedical "Big Data" challenge, and the complexity of healthcare data only compounds the problem to the point that coherent representation of both systems on the same platform seems insuperably difficult. We investigated the capability for complex, integrative genomic and clinical queries to be supported in the Informatics for Integrating Biology and the Bedside (i2b2) translational software package. Three different data integration approaches were developed: The first is based on Sequence Ontology, the second is based on the tranSMART engine, and the third on CouchDB. These novel methods for representing and querying complex genomic and clinical data on the i2b2 platform are available today for advancing precision medicine.

Original languageEnglish
Pages (from-to)e0172187
JournalPLoS One
Volume12
Issue number4
DOIs
Publication statusPublished - Apr 2017

Keywords

  • Journal Article

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    Murphy, S. N., Avillach, P., Bellazzi, R., Phillips, L., Gabetta, M., Eran, A., McDuffie, M. T., & Kohane, I. S. (2017). Combining clinical and genomics queries using i2b2 - Three methods. PLoS One, 12(4), e0172187. https://doi.org/10.1371/journal.pone.0172187