A tuberculosis ontology for host systems biology.

Journal: Tuberculosis (Edinburgh, Scotland)
Published Date: Jun 30, 2015

Abstract

A major hurdle facing tuberculosis (TB) investigators who want to utilize a rapidly growing body of data from both systems biology approaches and omics technologies is the lack of a standard vocabulary for data annotation and reporting. Lacking a means to readily compare samples from different research groups, a significant quantity of potentially informative data is largely ignored by researchers. To facilitate standardizing data across studies, a simple ontology of TB terms was developed to provide a common vocabulary for annotating data sets. New terminology was developed to address animal models and experimental systems, and existing clinically focused terminology was modified and adapted. This ontology can be used to annotate host TB data in public databases and collaborations, thereby standardizing database searches and allowing researchers to more easily compare results. To demonstrate the utility of a standard TB ontology for host systems biology, a web application was developed to annotate and compare human and animal model gene expression data sets.

Authors

  • David M Levine
    Department of Biostatistics, University of Washington, School of Public Health, Seattle, WA, USA.
  • Noton K Dutta
    Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
  • Josh Eckels
    LabKey Corporation, Seattle, WA, USA.
  • Charles Scanga
    Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA.
  • Catherine Stein
    Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA.
  • Smriti Mehra
    Department of Pathobiological Sciences, Louisiana State University School of Medicine, Baton Rouge, LA, USA; Tulane National Primate Research Center, Covington, LA, USA.
  • Deepak Kaushal
    Tulane National Primate Research Center, Covington, LA, USA.
  • Petros C Karakousis
    Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
  • Hugh Salamon
    Knowledge Synthesis Inc., Berkeley, CA, USA. Electronic address: hugh@knowledgesynthesis.com.

Keywords

External Resources

Popular Topics
Recent Journals