Choi Lab

Leena Choi, PhD
Professor of Biostatistics and Biomedical Informatics
Vice Chair of Diversity and Inclusion
Department of Biostatistics

The major research focus of our lab is to construct a system, called “EHR2PKPD”, for drug-related studies such as pharmacokinetics (PK), pharmacodynamics (PD), and pharmacogenomics (PGx) studies using electronic health records (EHRs). This system would allow to perform drug-related studie more efficiently by standardizing data extraction, data processing, and data building procedures. This system would provide a foundation for PK/PD-model guided clinical decision support systems embedded in EHRs to provide an optimal pharmacotherapy, the overarching goal of precision medicine.

The EHR2PKPD, a System for PK/PD Studies using EHRs.
Modified from Clin Pharm Ther 2020.
Extract-Med Pro-Med-NLP Pro-Med-Str Pro-Med-Str Pro-Drug-Level Pro-Laboratory Pro-Demographic Build-PK-Oral Build-PK-IV

EHR2PKPD is a modular system, divided into the three major procedures: data extraction (“Extract-”), data processing (“Pro-”), and data building (“Build-”). Modules were created or under development (gray color box) depending on the data element, task to perform, and type of PK/PD models.

For drugs with complex prescription pattern, dose data obtained from e-prescription databases may not be accurate enough to perform PK/PD studies. For these drugs, we may need to extract drug dose information from clinical notes using a natural language processing (NLP) system. We developed a flexible and targeted NLP system that can directly extract drug dose information from clinical notes, which was incorporated into our system (Extract-Med).

Building drug dose data from extracted dose information can be challenging. To address these challenges, we developed a dose data building algorithm that was implemented in our system (Pro-Med-NLP).

For drugs with simple prescription pattern, dose data can be relatively easily extracted from e-prescription databases and processed using Pro-Med-Str module.

Other data elements such as drug levels (Pro-Drug Level), demographics (Pro-Demographic), and laboratory data (Pro-Laboratory) can be processed using our system. These data can be combined with processed dose data to build PK/PD data using PK/PD data building modules (e.g., Build-PK-IV, Build-PK-Oral).


Lab Team

Cole Beck Marisa Blackman Elizabeth McNeer Michael Williams

Lab Alumni

Hannah L. Weeks Nathan T. James


  1. Choi L, Beck C, McNeer E, Weeks HL, Williams ML, James NT, Niu X, Abou-Khalil BW, Birdwell KA, Roden DM, Stein CM. Development of a System for Post-marketing Population Pharmacokinetic and Pharmacodynamic Studies using Real-World Data from Electronic Health Records. Clinical Pharmacology & Therapeutics. 2020 Apr;107(4):934-43. doi: 10.1002/cpt.1787.


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