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

doi:10.1371/journal.pone.0172187

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 journal › Article › peer-review

23 Scopus citations

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 highthroughput 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 language	English
Article number	e0172187
Journal	PLoS ONE
Volume	12
Issue number	4
DOIs	https://doi.org/10.1371/journal.pone.0172187
State	Published - 1 Apr 2017
Externally published	Yes

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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 highthroughput 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.",

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AU - Eran, Alal

AU - McDuffie, Michael T.

AU - Kohane, Isaac S.

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Combining clinical and genomics queries using i2b2 - Three methods

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