title: A tuberculosis ontology for host systems biology.
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.affiliation: Department of Biostatistics, University of Washington, School of Public Health, Seattle, WA, USA.
authors.forename: David M
authors.initials: DM
authors.lastname: Levine
authors.affiliation: Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
authors.forename: Noton K
authors.initials: NK
authors.lastname: Dutta
authors.affiliation: LabKey Corporation, Seattle, WA, USA.
authors.forename: Josh
authors.initials: J
authors.lastname: Eckels
authors.affiliation: Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA.
authors.forename: Charles
authors.initials: C
authors.lastname: Scanga
authors.affiliation: Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA.
authors.forename: Catherine
authors.initials: C
authors.lastname: Stein
authors.affiliation: Department of Pathobiological Sciences, Louisiana State University School of Medicine, Baton Rouge, LA, USA; Tulane National Primate Research Center, Covington, LA, USA.
authors.forename: Smriti
authors.initials: S
authors.lastname: Mehra
authors.affiliation: Tulane National Primate Research Center, Covington, LA, USA.
authors.forename: Deepak
authors.initials: D
authors.lastname: Kaushal
authors.affiliation: Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
authors.forename: Petros C
authors.initials: PC
authors.lastname: Karakousis
authors.affiliation: Knowledge Synthesis Inc., Berkeley, CA, USA. Electronic address: hugh@knowledgesynthesis.com.
authors.forename: Hugh
authors.initials: H
authors.lastname: Salamon
mesh_terms: D000818:Animals; D030541:Databases, Genetic / Q000592:standards*; D020869:Gene Expression Profiling / Q000592:standards*; D005786:Gene Expression Regulation; D063990:Gene Ontology; D005819:Genetic Markers; D054884:Host-Pathogen Interactions; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000235:genetics* / Q000472:pathogenicity; D049490:Systems Biology / Q000592:standards*; D009626:Terminology as Topic; D059467:Transcriptome; D014376:Tuberculosis / Q000235:genetics* / Q000382:microbiology
chemical_list: D005819:Genetic Markers
keywords: GEO; Gene expression; Mycobacterium; Ontology; Transcriptomics