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

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.

ROMOP: a light-weight R package for interfacing with OMOP-formatted electronic health record data.

OBJECTIVES: Electronic health record (EHR) data are increasingly used for biomedical discoveries. The nature of the data, however, requires expertise in both data science and EHR structure. The Observational Medical Out-comes Partnership (OMOP) common data model (CDM) standardizes the language and structure of EHR data to promote interoperability of EHR data for research. While the OMOP CDM is valuable and more attuned to research purposes, it still requires extensive domain knowledge to utilize effectively, potentially limiting more widespread adoption of EHR data for research and quality improvement. MATERIALS AND METHODS: We have created ROMOP: an R package for direct interfacing with EHR data in the OMOP CDM format. RESULTS: ROMOP streamlines typical EHR-related data processes. Its functions include exploration of data types, extraction and summarization of patient clinical and demographic data, and patient searches using any CDM vocabulary concept. CONCLUSION: ROMOP is freely available under the Massachusetts Institute of Technology (MIT) license and can be obtained from GitHub (http://github.com/BenGlicksberg/ROMOP). We detail instructions for setup and use in the Supplementary Materials. Additionally, we provide a public sandbox server containing synthesized clinical data for users to explore OMOP data and ROMOP (http://romop.ucsf.edu).

Leveraging a Statewide Clinical Data Warehouse to Expand Boundaries of the Learning Health System.

Learning Health Systems (LHS) require accessible, usable health data and a culture of collaboration-a challenge for any single system, let alone disparate organizations, with macro- and micro-systems. Recently, the National Science Foundation described this important setting as a cyber-social ecosystem. In 2004, in an effort to create a platform for transforming health in South Carolina, Health Sciences South Carolina (HSSC) was established as a research collaboration of the largest health systems, academic medical centers and research intensive universities in South Carolina. With work beginning in 2010, HSSC unveiled an integrated Clinical Data Warehouse (CDW) in 2013 as a crucial anchor to a statewide LHS. This CDW integrates data from independent health systems in near-real time, and harmonizes the data for aggregation and use in research. With records from over 2.7 million unique patients spanning 9 years, this multi-institutional statewide clinical research repository allows integrated individualized patient-level data to be used for multiple population health and biomedical research purposes. In the first 21 months of operation, more than 2,800 de-identified queries occurred through i2b2, with 116 users. HSSC has developed and implemented solutions to complex issues emphasizing anti-competitiveness and participatory governance, and serves as a recognized model to organizations working to improve healthcare quality by extending the traditional borders of learning health systems.