The Metabolomics Standards Initiative (MSI) guidelines were first published in 2007. These guidelines provided reporting standards for all stages of metabolomics analysis: experimental design, biological context, chemical analysis and data processing. Since 2012, a series of public metabolomics databases and repositories, which accept the deposition of metabolomic datasets, have arose. In this study, the compliance of 399 public data sets, from four major metabolomics data repositories, to the biological context MSI reporting standards were evaluated. None of the reporting standards were complied with in every publicly available study, although adherence rates varied greatly, from 0 to 97%. The plant minimum reporting standards were the most complied with and the microbial and in vitro were the least. Our results indicate the need for reassessment and revision of the existing MSI reporting standards.
This analysis code is to accompany the paper: Compliance with minimum information guidelines in public metabolomics repositories.
Analysis files are in the folder analysis-code. Use raw git to view HTML output files.
All analysis was performed using R version 3.3.2. The following packages were used ggplot2 version 2.2.1, xlsx version 0.5.7 and FSA version 0.8.13.
The analysis code can be found in analysis-code/analysis_MSIcompliance.Rmd. The R Markdown file was generated using knitr version 1.16.
The html output can be viewed on rawgit.