Compliance with minimum information guidelines in public metabolomics repositories

Rachel A Spicer,Reza Salek,Christoph Steinbeck

doi:10.1038/sdata.2017.137

Rachel A Spicer, Reza Salek + Show 1 more

Open Access

https://doi.org/10.1038/sdata.2017.137

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Abstract

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 arisen. In this study, the compliance of 399 public data sets, from four major metabolomics data repositories, to the biological context MSI reporting standards was 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.

Highlights

Leading members of the metabolomics community organised the development of the Metabolomics Standards Initiative (MSI), following examples from other communities[1,2], in 2005
Each report consists of the minimum reporting standards required for each class of experiment, as agreed upon by the MSI subgroup
Our results show that the level of compliance to the different sets of reporting standards varies greatly across public repositories

Summary

Introduction

Leading members of the metabolomics community organised the development of the Metabolomics Standards Initiative (MSI), following examples from other communities[1,2], in 2005. This work built on earlier efforts by the Standard Metabolic Reporting Structure initiative[3] and the Architecture for Metabolomics consortium (ArMet)[4]. Under the umbrella of the MSI5,6 working groups for biological context metadata, chemical analysis, data processing, ontology and data exchange were formed. These working groups published a series of reports, with minimal reporting standard recommendations for each area. During the early phase of this emerging network of global data exchange, the COordination of Standards in MetabOlomicS (COSMOS) consortium[12] was instrumental in filling some of the gaps in data standards and data formats. The MetabolomeXchange consortium that was based upon the successful ProteomeXchange[13] was founded through the COSMOS consortium

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