The NIAID TB Portals Program (TBPP) established a unique and growing database repository of socioeconomic, geographic, clinical, laboratory, radiological, and genomic data from patient cases of drug-resistant tuberculosis (DR-TB). Currently, there are 2,428 total cases from nine country sites (Azerbaijan, Belarus, Moldova, Georgia, Romania, China, India, Kazakhstan, and South Africa), 1,611 (66%) of which are multidrug- or extensively-drug resistant and 1,185 (49%), 863 (36%), and 952 (39%) of which contain X-ray, computed tomography (CT) scan, and genomic data, respectively. We introduce the Data Exploration Portal (TB DEPOT, https://depot.tbportals.niaid.nih.gov ) to visualize and analyze these multi-domain data. The TB DEPOT leverages the TBPP integration of clinical, socioeconomic, genomic, and imaging data into standardized formats and enables user-driven, repeatable, and reproducible analyses. It furthers the TBPP goals to provide a web-enabled analytics platform to countries with a high burden of multidrug-resistant TB (MDR-TB) but limited IT resources and inaccessible data, and enables the reusability of data, in conformity with the NIH’s Findable, Accessible, Interoperable, and Reusable (FAIR) principles. TB DEPOT provides access to “analysis-ready” data and the ability to generate and test complex clinically-oriented hypotheses instantaneously with minimal statistical background and data processing skills. TB DEPOT is also promising for enhancing medical training and furnishing well annotated, hard to find, MDR-TB patient cases. TB DEPOT, as part of TBPP, further fosters collaborative research efforts to better understand drug-resistant tuberculosis and aid in the development of novel diagnostics and personalized treatment regimens.
Objective Clinical research informatics tools are necessary to support comprehensive studies of infectious diseases. The National Institute of Allergy and Infectious Diseases (NIAID) developed the publicly accessible Tuberculosis Data Exploration Portal (TB DEPOT) to address the complex etiology of tuberculosis (TB). Materials and Methods TB DEPOT displays deidentified patient case data and facilitates analyses across a wide range of clinical, socioeconomic, genomic, and radiological factors. The solution is built using Amazon Web Services cloud-based infrastructure, .NET Core, Angular, Highcharts, R, PLINK, and other custom-developed services. Structured patient data, pathogen genomic variants, and medical images are integrated into the solution to allow seamless filtering across data domains. Results Researchers can use TB DEPOT to query TB patient cases, create and save patient cohorts, and execute comparative statistical analyses on demand. The tool supports user-driven data exploration and fulfills the National Institute of Health’s Findable, Accessible, Interoperable, and Reusable (FAIR) principles. Discussion TB DEPOT is the first tool of its kind in the field of TB research to integrate multidimensional data from TB patient cases. Its scalable and flexible architectural design has accommodated growth in the data, organizations, types of data, feature requests, and usage. Use of client-side technologies over server-side technologies and prioritizing maintenance have been important lessons learned. Future directions are dynamically prioritized and key functionality is shared through an application programming interface. Conclusion This paper describes the platform development methodology, resulting functionality, benefits, and technical considerations of a clinical research informatics application to support increased understanding of TB.
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