Ontology-based metabolomics data integration with quality control

Patricia Buendia, Ray M. Bradley, Thomas J. Taylor, Emma L. Schymanski, Gary J. Patti, Mansur R. Kabuka

Research output: Contribution to journalArticle

Abstract

Aim: The complications that arise when performing meta-analysis of datasets from multiple metabolomics studies are addressed with computational methods that ensure data quality, completeness of metadata and accurate interpretation across studies. Results & methodology: This paper presents an integrated system of quality control (QC) methods to assess metabolomics results by evaluating the data acquisition strategies and metabolite identification process when integrating datasets for meta-analysis. An ontology knowledge base and a rule-based system representing the experiment and chemical background information direct the processes involved in data integration and QC verification. A diabetes meta-analysis study using these QC methods finds putative biomarkers that differ between cohorts. Conclusion: The methods presented here ensure the validity of meta-analysis when integrating data from different metabolic profiling studies.

Original languageEnglish (US)
Pages (from-to)1139-1155
Number of pages17
JournalBioanalysis
Volume11
Issue number12
DOIs
StatePublished - Jan 1 2019
Externally publishedYes

Fingerprint

Metabolomics
Data integration
Quality Control
Quality control
Ontology
Meta-Analysis
Knowledge based systems
Biomarkers
Medical problems
Metabolites
Computational methods
Metadata
Knowledge Bases
Data acquisition
Experiments
Datasets
Data Accuracy

Keywords

  • data integration
  • diabetes use case
  • meta-analysis
  • metabolomics
  • ontology-based expert system
  • quality control

ASJC Scopus subject areas

  • Analytical Chemistry
  • Pharmacology, Toxicology and Pharmaceutics(all)
  • Clinical Biochemistry
  • Medical Laboratory Technology

Cite this

Buendia, P., Bradley, R. M., Taylor, T. J., Schymanski, E. L., Patti, G. J., & Kabuka, M. R. (2019). Ontology-based metabolomics data integration with quality control. Bioanalysis, 11(12), 1139-1155. https://doi.org/10.4155/bio-2018-0303

Ontology-based metabolomics data integration with quality control. / Buendia, Patricia; Bradley, Ray M.; Taylor, Thomas J.; Schymanski, Emma L.; Patti, Gary J.; Kabuka, Mansur R.

In: Bioanalysis, Vol. 11, No. 12, 01.01.2019, p. 1139-1155.

Research output: Contribution to journalArticle

Buendia, P, Bradley, RM, Taylor, TJ, Schymanski, EL, Patti, GJ & Kabuka, MR 2019, 'Ontology-based metabolomics data integration with quality control', Bioanalysis, vol. 11, no. 12, pp. 1139-1155. https://doi.org/10.4155/bio-2018-0303
Buendia P, Bradley RM, Taylor TJ, Schymanski EL, Patti GJ, Kabuka MR. Ontology-based metabolomics data integration with quality control. Bioanalysis. 2019 Jan 1;11(12):1139-1155. https://doi.org/10.4155/bio-2018-0303
Buendia, Patricia ; Bradley, Ray M. ; Taylor, Thomas J. ; Schymanski, Emma L. ; Patti, Gary J. ; Kabuka, Mansur R. / Ontology-based metabolomics data integration with quality control. In: Bioanalysis. 2019 ; Vol. 11, No. 12. pp. 1139-1155.
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