A tuberculosis ontology for host systems biology

David M. Levine, Noton Dutta, Josh Eckels, Charles Scanga, Catherine Stein, Smriti Mehra, Deepak Kaushal, Petros Karakousis, Hugh Salamon

Research output: Contribution to journalArticle

Abstract

Summary 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.

Original languageEnglish (US)
Pages (from-to)570-574
Number of pages5
JournalTuberculosis
Volume95
Issue number5
DOIs
StatePublished - Sep 1 2015

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Systems Biology
Tuberculosis
Vocabulary
Research Personnel
Terminology
Animal Models
Databases
Information Systems
Research Design
Technology
Gene Expression
Research
Datasets

Keywords

  • Gene expression
  • GEO
  • Mycobacterium
  • Ontology
  • Transcriptomics

ASJC Scopus subject areas

  • Microbiology
  • Immunology
  • Infectious Diseases
  • Microbiology (medical)

Cite this

Levine, D. M., Dutta, N., Eckels, J., Scanga, C., Stein, C., Mehra, S., ... Salamon, H. (2015). A tuberculosis ontology for host systems biology. Tuberculosis, 95(5), 570-574. https://doi.org/10.1016/j.tube.2015.05.012

A tuberculosis ontology for host systems biology. / Levine, David M.; Dutta, Noton; Eckels, Josh; Scanga, Charles; Stein, Catherine; Mehra, Smriti; Kaushal, Deepak; Karakousis, Petros; Salamon, Hugh.

In: Tuberculosis, Vol. 95, No. 5, 01.09.2015, p. 570-574.

Research output: Contribution to journalArticle

Levine, DM, Dutta, N, Eckels, J, Scanga, C, Stein, C, Mehra, S, Kaushal, D, Karakousis, P & Salamon, H 2015, 'A tuberculosis ontology for host systems biology', Tuberculosis, vol. 95, no. 5, pp. 570-574. https://doi.org/10.1016/j.tube.2015.05.012
Levine DM, Dutta N, Eckels J, Scanga C, Stein C, Mehra S et al. A tuberculosis ontology for host systems biology. Tuberculosis. 2015 Sep 1;95(5):570-574. https://doi.org/10.1016/j.tube.2015.05.012
Levine, David M. ; Dutta, Noton ; Eckels, Josh ; Scanga, Charles ; Stein, Catherine ; Mehra, Smriti ; Kaushal, Deepak ; Karakousis, Petros ; Salamon, Hugh. / A tuberculosis ontology for host systems biology. In: Tuberculosis. 2015 ; Vol. 95, No. 5. pp. 570-574.
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