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Quantitative Biology

, Volume 5, Issue 4, pp 291–301 | Cite as

The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines

  • Jie Zheng
  • Huan Li
  • Qingzhi Liu
  • Yongqun He
Research Article
  • 132 Downloads

Abstract

Background

The community-based Ontology of Biological and Clinical Statistics (OBCS) represents and standardizes biological and clinical data and statistical methods.

Methods

Both OBCS and the Vaccine Ontology (VO) were used to ontologically model various components and relations in a typical host response to vaccination study. Such a model was then applied to represent and compare three microarray studies of host responses to the yellow fever vaccine YF-17D. A literature meta-analysis was then conducted to survey yellow fever vaccine response papers and summarize statistical methods, using OBCS.

Results

A general ontological model was developed to identify major components in a typical host response to vaccination. Our ontology modeling of three similar studies identified common and different components which may contribute to varying conclusions. Although these three studies all used the same vaccine, human blood samples, similar sample collection time post vaccination, and microarray assays, statistically differentially expressed genes and associated gene functions differed, likely due to the differences in specific variables (e.g., microarray type and human variations). Our manual annotation of 95 papers in human responses to yellow fever vaccines identified 38 data analysis methods. These statistical methods were consistently represented and classified with OBCS. Eight statistical methods not available in existing ontologies were added to OBCS.

Conclusions

The study represents the first single use case of applying OBCS ontology to standardize, integrate, and use biomedical data and statistical methods. Our ontology-based meta-analysis showed that different experimental results might be due to different experimental assays and conditions, sample variations, and data analysis methods.

Keywords

OBCS ontology vaccine host response to vaccination statistical data analysis 

Notes

Acknowledgements

The development of VO and OBCS and the vaccine modeling research was supported by a grant from the USA National Institute of Allergy and Infectious Diseases (NIAID) (R01AI081062). We appreciate Mr. Omar Tibi’s proofreading and editorial changes of this manuscript.

Supplementary material

40484_2017_122_MOESM1_ESM.pdf (144 kb)
Supplement Table 1: Statistical method annotated using OBCS

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Copyright information

© Higher Education Press and Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  1. 1.Department of GeneticsUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaUSA
  2. 2.Health Science CenterShenzhen UniversityShenzhenChina
  3. 3.Department of MathematicsUniversity of MarylandCollege ParkUSA
  4. 4.Unit for Laboratory Animal MedicineUniversity of Michigan Medical SchoolAnn ArborUSA
  5. 5.Department of Microbiology and ImmunologyUniversity of Michigan Medical SchoolAnn ArborUSA
  6. 6.Center for Computational Medicine and BioinformaticsUniversity of Michigan Medical SchoolAnn ArborUSA
  7. 7.Comprehensive Cancer CenterUniversity of Michigan Medical SchoolAnn ArborUSA

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