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Ruhamyankaka E, Brunk BP, Dorsey G, et al. ClinEpiDB: an open-access clinical epidemiology database resource encouraging online exploration of complex studies. Gates Open Res. 2020;3:1661doi: 10.12688/gatesopenres.13087.2.
Ruhamyankaka, E., Brunk, B. P., Dorsey, G., Harb, O. S., Helb, D. A., Judkins, J., Kissinger, J. C., Lindsay, B., Roos, D. S., San, E. J., Stoeckert, C. J., Zheng, J., & Tomko, S. S. (2019). ClinEpiDB: an open-access clinical epidemiology database resource encouraging online exploration of complex studies. Gates open research, 31661. https://doi.org/10.12688/gatesopenres.13087.2
Ruhamyankaka, Emmanuel, et al. "ClinEpiDB: an open-access clinical epidemiology database resource encouraging online exploration of complex studies." Gates open research vol. 3 (2019): 1661. doi: https://doi.org/10.12688/gatesopenres.13087.2
Ruhamyankaka E, Brunk BP, Dorsey G, Harb OS, Helb DA, Judkins J, Kissinger JC, Lindsay B, Roos DS, San EJ, Stoeckert CJ, Zheng J, Tomko SS. ClinEpiDB: an open-access clinical epidemiology database resource encouraging online exploration of complex studies. Gates Open Res. 2020 Apr 06;3:1661. doi: 10.12688/gatesopenres.13087.2. eCollection 2019. PMID: 32047873; PMCID: PMC6993508.
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Gates Open Res. 2020 Apr 06;3:1661. doi: 10.12688/gatesopenres.13087.2. eCollection 2019.

ClinEpiDB: an open-access clinical epidemiology database resource encouraging online exploration of complex studies.

Gates open research

Emmanuel Ruhamyankaka, Brian P Brunk, Grant Dorsey, Omar S Harb, Danica A Helb, John Judkins, Jessica C Kissinger, Brianna Lindsay, David S Roos, Emmanuel James San, Christian J Stoeckert, Jie Zheng, Sheena Shah Tomko

Affiliations

  1. Infectious Diseases Research Collaboration, Kampala, Uganda.
  2. Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
  3. Department of Medicine, San Francisco General Hospital, University of California, San Francisco, CA, 94110, USA.
  4. Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA, 30602, USA.
  5. Department of Genetics, University of Georgia, Athens, GA, 30602, USA.
  6. Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.
  7. Kwazulu-Natal Research and Innovation Sequencing Platform, Durban, South Africa.
  8. Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA.
  9. Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, 19104, USA.

PMID: 32047873 PMCID: PMC6993508 DOI: 10.12688/gatesopenres.13087.2

Abstract

The concept of open data has been gaining traction as a mechanism to increase data use, ensure that data are preserved over time, and accelerate discovery. While epidemiology data sets are increasingly deposited in databases and repositories, barriers to access still remain. ClinEpiDB was constructed as an open-access online resource for clinical and epidemiologic studies by leveraging the extensive web toolkit and infrastructure of the Eukaryotic Pathogen Database Resources (EuPathDB; a collection of databases covering 170+ eukaryotic pathogens, relevant related species, and select hosts) combined with a unified semantic web framework. Here we present an intuitive point-and-click website that allows users to visualize and subset data directly in the ClinEpiDB browser and immediately explore potential associations. Supporting study documentation aids contextualization, and data can be downloaded for advanced analyses. By facilitating access and interrogation of high-quality, large-scale data sets, ClinEpiDB aims to spur collaboration and discovery that improves global health.

Copyright: © 2020 Ruhamyankaka E et al.

Keywords: ClinEpiDB; Data visualization; Enteric disease; Epidemiology database; FAIR data; Infectious diseases; Malaria

Conflict of interest statement

No competing interests were disclosed.

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