A decade after the metabolomics standards initiative it's time for a revision.
A decade after the metabolomics standards initiative it's time for a revision.
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DOI：
10.1038/sdata.2017.138
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发表时间：
2017-09-26
期刊：
影响因子：
9.8
通讯作者：
Steinbeck C
中科院分区：
文献类型：
--
作者：
Spicer RA;Salek R;Steinbeck C
最近对可公开获得的代谢组学数据的分析表明，在公开共享的代谢组学研究中，MSI指南没有得到很好的遵守。我们建议重新审视和修订代谢组学指南，就像在其他社区所做的那样，以适应当前社区的需要。2005年，代谢组学领域的主要专家在代谢组学学会的支持下，聚集在一起讨论代谢组学实验标准，并成立了代谢组学标准倡议(MSI)1。两年后，MSI发布了一系列代谢组学报告标准2-8。又过了5年，代谢组学数据的全球储存库网络9-11才出现，MSI指南可以应用于该网络。现在，截至2017年8月2日，有700多个代谢组学数据集通过代谢交换(http://www.)公开提供代谢物交换。Org/)，这是第一次允许对代谢组学数据共享和遵守MSI指南的情况进行评估。自MSI报告标准首次发布以来的十年中，代谢组学社区已经成熟。现在人们对遗传和环境因素有了更多的了解，这些因素可以对代谢组产生重大影响。通用代谢组学数据储存库MetbraLights 9和代谢组学工作台10，以及较小的更具体的储存库MetaPhen 12和Mery-B 13，旨在遵守MSI关于最低限度元数据报告的指导方针。我们已经进行了一项研究，评估了代谢光、代谢组学工作台、MetaPhen和Mery-B库中数据集的遵从性。结果发现，许多MSI的最低报告标准并未被这些存储库中的许多研究所遵循(图1显示了来自MetabLights存储库的示例)。在所有公开可获得的研究中，没有符合MSI标准的。然而，有一些最低报告标准并不适用于每项研究，例如，治疗，这只与包括治疗在内的研究有关。仅适用于一小部分研究可能导致符合这些标准的百分比较低(图1)。
A recent analysis of publicly available metabolomics data shows that the MSI guidelines are not well abided to in publicly shared metabolomics studies. We propose that the MSI guidelines should be revisited and revised, as has been done in other communities, to fit the current community needs.In the year 2005, leading experts in metabolomics, with support from the Metabolomics Society, gathered to discuss metabolomics experimental standards and formed the metabolomics standards initiative (MSI) 1. Two years later, the MSI published a series of reporting standards for metabolomics 2–8. Another 5 years passed until a network of global repositories 9–11 for metabolomics data arose, to which the MSI guidelines could be applied. Now, as of 2nd August 2017, there are more than 700 metabolomics datasets publicly available via MetabolomeXchange (http://www. metabolomexchange. org/), which, for the first time, allows for an assessment of metabolomics data sharing and compliance with the MSI guidelines. In the decade since the first publication of the MSI reporting standards, the metabolomics community has matured. There is now greater understanding of genetic and environmental factors that can induce significant effects on the metabolome. The general purpose metabolomics data repositories MetaboLights 9 and Metabolomics Workbench 10, along with the smaller more specific repositories, MetaPhen 12 and MeRy-B 13, were designed to adhere with the MSI guidelines for minimum metadata reporting. We have performed a study assessing the compliance of the datasets in the MetaboLights, Metabolomics Workbench, MetaPhen, and MeRy-B repositories. It was found that many of the MSI’s minimal reporting standards are not complied with by many of the studies in these repositories (Fig. 1 shows examples from the MetaboLights repository). There were no MSI standards that were complied with in every publicly available study. There are, however, minimal reporting standards that are not applicable to every study eg, treatment, which is only relevant to studies including a treatment. Being only applicable to a small subset of studies may result in the low percentage compliance to these standards (Fig. 1).
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影响因子：
14.9
作者：
Haug K;Salek RM;Conesa P;Hastings J;de Matos P;Rijnbeek M;Mahendraker T;Williams M;Neumann S;Rocca-Serra P;Maguire E;González-Beltrán A;Sansone SA;Griffin JL;Steinbeck C
通讯作者：
Steinbeck C
影响因子：
3.6
作者：
van der Werf, Mariet J.;Takors, Ralf;Smedsgaard, Jorn;Nielsen, Jens;Ferenci, Tom;Portais, Jean Charles;Wittmann, Christoph;Hooks, Mark;Tomassini, Alberta;Oldiges, Marco;Fostel, Jennifer;Sauer, Uwe
通讯作者：
Sauer, Uwe
DOI：
10.1016/j.csbj.2015.01.002
发表时间：
2015-01-01
影响因子：
6
作者：
Everett, Jeremy R.
通讯作者：
Everett, Jeremy R.
影响因子：
3.6
作者：
Fiehn, Oliver;Robertson, Don;Sansone, Susanna-Assunta
通讯作者：
Sansone, Susanna-Assunta
DOI：
10.1093/bioinformatics/btq415
发表时间：
2010-09-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Rocca-Serra P;Brandizi M;Maguire E;Sklyar N;Taylor C;Begley K;Field D;Harris S;Hide W;Hofmann O;Neumann S;Sterk P;Tong W;Sansone SA
通讯作者：
Sansone SA