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A Tool to Encourage Minimum Reporting Guideline Uptake for Data Analysis in Metabolomics

1
The Irish Centre for Fetal and Neonatal Translational Research (INFANT), Department of Obstetrics and Gynaecology, University College Cork, T12 YE02 Cork, Ireland
2
The International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372 Lyon CEDEX 08, France
*
Author to whom correspondence should be addressed.
Metabolites 2019, 9(3), 43; https://doi.org/10.3390/metabo9030043
Received: 22 January 2019 / Revised: 23 February 2019 / Accepted: 27 February 2019 / Published: 5 March 2019
(This article belongs to the Special Issue Metabolomics — Workflows, Methods and Applications)
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PDF [210 KB, uploaded 5 March 2019]

Abstract

Despite the proposal of minimum reporting guidelines for metabolomics over a decade ago, reporting on the data analysis step in metabolomics studies has been shown to be unclear and incomplete. Major omissions and a lack of logical flow render the data analysis’ sections in metabolomics studies impossible to follow, and therefore replicate or even imitate. Here, we propose possible reasons why the original reporting guidelines have had poor adherence and present an approach to improve their uptake. We present in this paper an R markdown reporting template file that guides the production of text and generates workflow diagrams based on user input. This R Markdown template contains, as an example in this instance, a set of minimum information requirements specifically for the data pre-treatment and data analysis section of biomarker discovery metabolomics studies, (gleaned directly from the original proposed guidelines by Goodacre at al). These minimum requirements are presented in the format of a questionnaire checklist in an R markdown template file. The R Markdown reporting template proposed here can be presented as a starting point to encourage the data analysis section of a metabolomics manuscript to have a more logical presentation and to contain enough information to be understandable and reusable. The idea is that these guidelines would be open to user feedback, modification and updating by the metabolomics community via GitHub. View Full-Text
Keywords: reproducibility; minimum guidelines; reporting; data analysis reproducibility; minimum guidelines; reporting; data analysis
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).
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Considine, E.C.; Salek, R.M. A Tool to Encourage Minimum Reporting Guideline Uptake for Data Analysis in Metabolomics. Metabolites 2019, 9, 43.

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