Special Communication
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

https://doi.org/10.1016/j.jbi.2019.103325Get rights and content
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Highlights

  • The Biomedical Data Translator Program was launched in October 2016.

  • The Biomedical Data Translator Consortium comprises 11 teams and ~200 team members.

  • Regular in-person hackathons have proven effective in promoting team science.

  • We describe a hackathon activity focused on open Translator clinical data sources.

  • Our ‘lessons learned’ have broad applicability across scientific domains.

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.

Keywords

Hackathon
Open data
Clinical data
Team science
Application programming interface
Multi-institutional collaboration

Abbreviations

API
Application Programming Interface
COHD
Columbia Open Health Data
CUIMC
Columbia University Irving Medical Center
EHR
electronic health record
FHIR
Health Level Seven International Fast Healthcare Interoperability Resources
ICEES
Integrated Clinical and Environmental Exposures Service
NCATS
National Center for Advancing Translational Sciences
PM2.5
Particulate matter of size ≤ 2.5-µm in diameter

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Apart from the lead and senior authors, all other authors are listed alphabetically. Specific author contributions are listed under ‘Author Contributions’.