1. Metabolomics resources in interoperability and Open-Science
- Author
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Rodriguez-Mier, Pablo, Low Yanwen, Dorrain, Manach, Claudine, Pujos-Guillot, Estelle, Giacomoni, Franck, Centro Singular de Investigacion en Tecnoloxias da Informacion (CiTIUS), Universidade de Santiago de Compostela [Spain] (USC ), University of Santiago de Compostela, Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Plateforme d'Exploration du Métabolisme, Institut National de la Recherche Agronomique (INRA), Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Plateforme Exploration du Métabolisme (PFEM), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-MetaboHUB-Clermont, MetaboHUB-MetaboHUB, and ProdInra, Archive Ouverte
- Subjects
[CHIM.ANAL] Chemical Sciences/Analytical chemistry ,[SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie ,[CHIM.ANAL]Chemical Sciences/Analytical chemistry ,metadata ,[SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie ,métadonnée ,[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] ,bioinformatique ,[INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM] ,analyse métabolomique - Abstract
Reproducibility and data sharing of metabolomic experiments are two fundamental issues that are needed to be addressed by the community in order to improve the quality of the research. Many advances have been made so far through different initiatives, among which are: 1) the minimal reporting standard defined by the Metabolomics Standards Initiative (MSI) for ensuring a minimal amount of information to support the interpretation of a metabolomics experiment; 2) metabolomic repositories such as MetaboLights or MetabolomeXchange for sharing experimental data and associated metadata across species; and 3) specific bioinformatic tools for reproducibility and data processing such as Workflow4Metabolomics (W4M), a reference workflow repository dedicated to metabolomics data processing. However there are still many issues that prevent to harness the full potential of metabolomics, such as incomplete or a partial adherence with guidelines or complex submission processes of experimental data. To address these limitations, in this work we extend W4M to help scientists in the definition and in the formatting of the whole collection of metadata coming from metabolomics based projects. For this purpose, we included new tools to acquire and transform in an user-friendly way metabolomics experimental raw data, study features and data analysis annotation, with the aim of assisting biologist in the incorporation of the minimal information for an experiment. This work will also generalize the use of the standard mzML format in W4M and the ISA Tab format for its posterior automatic submission ta MetaboLights, enhancing in this way the link between data providers and data managers.
- Published
- 2017