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National Institute of Environmental Health Sciences

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Your Environment. Your Health.

Publication Detail

Title: Sex, obesity, diabetes, and exposure to particulate matter among patients with severe asthma: Scientific insights from a comparative analysis of open clinical data sources during a five-day hackathon.

Authors: Fecho, Karamarie; Ahalt, Stanley C; Arunachalam, Saravanan; Champion, James; Chute, Christopher G; Davis, Sarah; Gersing, Kenneth; Glusman, Gustavo; Hadlock, Jennifer; Lee, Jewel; Pfaff, Emily; Robinson, Max; Sid, Eric; Ta, Casey; Xu, Hao; Zhu, Richard; Zhu, Qian; Peden, David B; Biomedical Data Translator Consortium

Published In J Biomed Inform, (2019 12)

Abstract: This special communication describes activities, products, and lessons learned from a recent hackathon that was funded by the National Center for Advancing Translational Sciences via the Biomedical Data Translator program ('Translator'). Specifically, Translator team members self-organized and worked together to conceptualize and execute, over a five-day period, a multi-institutional clinical research study that aimed to examine, using open clinical data sources, relationships between sex, obesity, diabetes, and exposure to airborne fine particulate matter among patients with severe asthma. The goal was to develop a proof of concept that this new model of collaboration and data sharing could effectively produce meaningful scientific results and generate new scientific hypotheses. Three Translator Clinical Knowledge Sources, each of which provides open access (via Application Programming Interfaces) to data derived from the electronic health record systems of major academic institutions, served as the source of study data. Jupyter Python notebooks, shared in GitHub repositories, were used to call the knowledge sources and analyze and integrate the results. The results replicated established or suspected relationships between sex, obesity, diabetes, exposure to airborne fine particulate matter, and severe asthma. In addition, the results demonstrated specific differences across the three Translator Clinical Knowledge Sources, suggesting cohort- and/or environment-specific factors related to the services themselves or the catchment area from which each service derives patient data. Collectively, this special communication demonstrates the power and utility of intense, team-oriented hackathons and offers general technical, organizational, and scientific lessons learned.

PubMed ID: 31676459 Exiting the NIEHS site

MeSH Terms: No MeSH terms associated with this publication

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