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A Checklist for Reproducible Computational Analysis in Clinical Metabolomics Research
Clinical metabolomics emerged as a novel approach for biomarker discovery with the translational potential to guide next-generation therapeutics and precision health interventions. However, reproducibility in clinical research employing metabolomics data is challenging. Checklists are a helpful tool...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8779534/ https://www.ncbi.nlm.nih.gov/pubmed/35050209 http://dx.doi.org/10.3390/metabo12010087 |
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author | Du, Xinsong Aristizabal-Henao, Juan J. Garrett, Timothy J. Brochhausen, Mathias Hogan, William R. Lemas, Dominick J. |
author_facet | Du, Xinsong Aristizabal-Henao, Juan J. Garrett, Timothy J. Brochhausen, Mathias Hogan, William R. Lemas, Dominick J. |
author_sort | Du, Xinsong |
collection | PubMed |
description | Clinical metabolomics emerged as a novel approach for biomarker discovery with the translational potential to guide next-generation therapeutics and precision health interventions. However, reproducibility in clinical research employing metabolomics data is challenging. Checklists are a helpful tool for promoting reproducible research. Existing checklists that promote reproducible metabolomics research primarily focused on metadata and may not be sufficient to ensure reproducible metabolomics data processing. This paper provides a checklist including actions that need to be taken by researchers to make computational steps reproducible for clinical metabolomics studies. We developed an eight-item checklist that includes criteria related to reusable data sharing and reproducible computational workflow development. We also provided recommended tools and resources to complete each item, as well as a GitHub project template to guide the process. The checklist is concise and easy to follow. Studies that follow this checklist and use recommended resources may facilitate other researchers to reproduce metabolomics results easily and efficiently. |
format | Online Article Text |
id | pubmed-8779534 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-87795342022-01-22 A Checklist for Reproducible Computational Analysis in Clinical Metabolomics Research Du, Xinsong Aristizabal-Henao, Juan J. Garrett, Timothy J. Brochhausen, Mathias Hogan, William R. Lemas, Dominick J. Metabolites Review Clinical metabolomics emerged as a novel approach for biomarker discovery with the translational potential to guide next-generation therapeutics and precision health interventions. However, reproducibility in clinical research employing metabolomics data is challenging. Checklists are a helpful tool for promoting reproducible research. Existing checklists that promote reproducible metabolomics research primarily focused on metadata and may not be sufficient to ensure reproducible metabolomics data processing. This paper provides a checklist including actions that need to be taken by researchers to make computational steps reproducible for clinical metabolomics studies. We developed an eight-item checklist that includes criteria related to reusable data sharing and reproducible computational workflow development. We also provided recommended tools and resources to complete each item, as well as a GitHub project template to guide the process. The checklist is concise and easy to follow. Studies that follow this checklist and use recommended resources may facilitate other researchers to reproduce metabolomics results easily and efficiently. MDPI 2022-01-17 /pmc/articles/PMC8779534/ /pubmed/35050209 http://dx.doi.org/10.3390/metabo12010087 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Review Du, Xinsong Aristizabal-Henao, Juan J. Garrett, Timothy J. Brochhausen, Mathias Hogan, William R. Lemas, Dominick J. A Checklist for Reproducible Computational Analysis in Clinical Metabolomics Research |
title | A Checklist for Reproducible Computational Analysis in Clinical Metabolomics Research |
title_full | A Checklist for Reproducible Computational Analysis in Clinical Metabolomics Research |
title_fullStr | A Checklist for Reproducible Computational Analysis in Clinical Metabolomics Research |
title_full_unstemmed | A Checklist for Reproducible Computational Analysis in Clinical Metabolomics Research |
title_short | A Checklist for Reproducible Computational Analysis in Clinical Metabolomics Research |
title_sort | checklist for reproducible computational analysis in clinical metabolomics research |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8779534/ https://www.ncbi.nlm.nih.gov/pubmed/35050209 http://dx.doi.org/10.3390/metabo12010087 |
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