PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model

Abstract

Motivation: Electronic health records (EHRs) are quickly becoming omnipresent in healthcare, but interoperability issues and technical demands limit their use for biomedical and clinical research. Interactive and flexible software that interfaces directly with EHR data structured around a common data model (CDM) could accelerate more EHR-based research by making the data more accessible to researchers who lack computational expertise and/or domain knowledge.

Results: We present PatientExploreR, an extensible application built on the R/Shiny framework that interfaces with a relational database of EHR data in the Observational Medical Outcomes Partnership CDM format. PatientExploreR produces patient-level interactive and dynamic reports and facilitates visualization of clinical data without any programming required. It allows researchers to easily construct and export patient cohorts from the EHR for analysis with other software. This application could enable easier exploration of patient-level data for physicians and researchers. PatientExploreR can incorporate EHR data from any institution that employs the CDM for users with approved access. The software code is free and open source under the MIT license, enabling institutions to install and users to expand and modify the application for their own purposes.

Availability and implementation: PatientExploreR can be freely obtained from GitHub: https://github.com/BenGlicksberg/PatientExploreR. We provide instructions for how researchers with approved access to their institutional EHR can use this package. We also release an open sandbox server of synthesized patient data for users without EHR access to explore: http://patientexplorer.ucsf.edu.

Supplementary information: Supplementary data are available at Bioinformatics online.

Fig. 1.

Basic functionality of PatientExploreR (see Supplementary Figures for more details). PatientExploreR allows for dynamic exploration and visualization of cohort and patient-level EHR data in OMOP format. Users can query for cohorts using combinations of any CDM vocabulary concept in any domain. Users can visualize and export outputs of this search. Once a patient is selected, a full report of all clinical concepts can be browsed and exported. Further, users can dynamically explore encounters and clinical concepts over time in both interactive numeric line and timeline plots. Further, users can interactively plot multiple modalities at once in the Multiplex Data Explorer section