Journal
METABOLOMICS
Volume 12, Issue 1, Pages -Publisher
SPRINGER
DOI: 10.1007/s11306-015-0879-3
Keywords
Metabolomics; Data standards; Mass spectrometry; NMR; Experimental metadata; Data sharing
Categories
Funding
- European Commission COSMOS Grant [EC312941]
- European Commission PhenoMeNal Grant [EC654241]
- Institut Francais de Bioinformatique (IFB) grant PIA INBS
- UK BBSRC [BB/I000933/1, BB/L024152/1, BB/K021125/1]
- MRC [MR/L01632X/1]
- Australian National Collaborative Research Infrastructure Strategy
- BBSRC [BB/L024101/1, BB/J020265/1, BB/L005069/1]
- University of Oxford e-Research Centre
- K BBSRC Grant [BB/L024101/1]
- BBSRC [BB/L024152/1, BB/K021125/1, BB/M027635/1, BB/I000771/1, BB/I025840/1, BB/M027252/1, BB/I000933/1, BB/H024921/1, BB/E025080/1] Funding Source: UKRI
- MRC [MC_EX_G0800783] Funding Source: UKRI
- Biotechnology and Biological Sciences Research Council [BB/M027252/1, BB/E025080/1, BB/L005069/1, BB/J020265/1, BB/H024921/1, BB/I000933/1, BB/L024101/1, BB/L024152/1, BB/M027635/1, BB/I025840/1, BB/K021125/1, BB/I000771/1] Funding Source: researchfish
- Medical Research Council [MR/L01632X/1, MC_EX_G0800783] Funding Source: researchfish
- Grants-in-Aid for Scientific Research [15K21738, 15H05898] Funding Source: KAKEN
Ask authors/readers for more resources
Thousands of articles using metabolomics approaches are published every year. With the increasing amounts of data being produced, mere description of investigations as text in manuscripts is not sufficient to enable re-use anymore: the underlying data needs to be published together with the findings in the literature to maximise the benefit from public and private expenditure and to take advantage of an enormous opportunity to improve scientific reproducibility in metabolomics and cognate disciplines. Reporting recommendations in metabolomics started to emerge about a decade ago and were mostly concerned with inventories of the information that had to be reported in the literature for consistency. In recent years, metabolomics data standards have developed extensively, to include the primary research data, derived results and the experimental description and importantly the metadata in a machine-readable way. This includes vendor independent data standards such as mzML for mass spectrometry and nmrML for NMR raw data that have both enabled the development of advanced data processing algorithms by the scientific community. Standards such as ISA-Tab cover essential metadata, including the experimental design, the applied protocols, association between samples, data files and the experimental factors for further statistical analysis. Altogether, they pave the way for both reproducible research and data reuse, including meta-analyses. Further incentives to prepare standards compliant data sets include new opportunities to publish data sets, but also require a little arm twisting'' in the author guidelines of scientific journals to submit the data sets to public repositories such as the NIH Metabolomics Workbench or MetaboLights at EMBL-EBI. In the present article, we look at standards for data sharing, investigate their impact in metabolomics and give suggestions to improve their adoption.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available