Setup X-a public study design database for metabolomic projects

Martin Scholz, Oliver Fiehn

Research output: Chapter in Book/Report/Conference proceedingConference contribution

100 Scopus citations

Abstract

Metabolomic databases are useless without accurate description of the biological study design and accompanying metadata reporting on the laboratory workflow from sample preparation to data processing. Here we report on the implementation of a database system that enables investigators to detail and set up a biological experiment, and that also steers laboratory workflows by direct access to the data acquisition instrument. SetupX utilizes orthogonal biological parameters such as genotype, organ, and treatment(s) for delineating the dimensions of a study which define the number of classes under investigation. Publicly available taxonomic and ontology repositories are utilized to ensure data integrity and logic consistency of class designs. Class descriptions are subsequently employed to schedule and randomize data acquisitions, and to deploy metabolite annotations carried out by the seamlessly integrated mass spectrometry database, BinBase. Annotated result data files are housed by SetupX for downloads and queries. Currently, 39 users have generated 48 studies, some of which are made public.

Original languageEnglish (US)
Title of host publicationPacific Symposium on Biocomputing 2007, PSB 2007
Pages169-180
Number of pages12
StatePublished - 2007
EventPacific Symposium on Biocomputing, PSB 2007 - Maui, HI, United States
Duration: Jan 3 2007Jan 7 2007

Other

OtherPacific Symposium on Biocomputing, PSB 2007
CountryUnited States
CityMaui, HI
Period1/3/071/7/07

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Biomedical Engineering
  • Medicine(all)

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  • Cite this

    Scholz, M., & Fiehn, O. (2007). Setup X-a public study design database for metabolomic projects. In Pacific Symposium on Biocomputing 2007, PSB 2007 (pp. 169-180)