Metadata harmonization–Standards are the key for a better usage of omics data for integrative microbiome analysis
2022
Cernava, Tomislav | Rybakova, Daria | Buscot, François | Clavel, Thomas | Mchardy, Alice Carolyn | Meyer, Fernando | Meyer, Folker | Overmann, Jörg | Stecher, Bärbel | Sessitsch, Angela | Schloter, Michael | Berg, Gabriele | Arruda, Paulo | Bartzanas, Thomas | Champomier-Verges, Marie-Christine | Charles, Trevor | Maguin, Emmanuelle | Graz University of Technology [Graz] (TU Graz) | German Centre for Integrative Biodiversity Research (iDiv) | Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ) | Universitätsklinikum RWTH Aachen - University Hospital Aachen [Aachen, Germany] (UKA) ; RWTH Aachen University = Rheinisch-Westfälische Technische Hochschule Aachen (RWTH Aachen) | German Center for Infection Research - Partner Site Bonn-Cologne (DZIF) | Medizinische Hochschule Hannover = Hannover Medical School (MHH) | Helmholtz Centre for Infection Research (HZI) | Technische Universität Braunschweig = Technical University of Braunschweig [Braunschweig] | Universität Duisburg-Essen = University of Duisburg-Essen [Essen] | Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ) | German Center for Infection Research - partner site Hannover-Braunschweig (DZIF) | German Center for Infection Research, Partnersite Munich (DZIF) | Austrian Institute of Technology [Vienna] (AIT) | Institute of Biomathematics and Biometry - Helmholtz Zentrum München (IBB) ; Helmholtz Zentrum München = German Research Center for Environmental Health (HMGU) | University of Potsdam = Universität Potsdam | Universidade Estadual de Campinas = University of Campinas (UNICAMP) | Agricultural University of Athens | MICrobiologie de l'ALImentation au Service de la Santé (MICALIS) ; AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) | University of Waterloo [Waterloo]
International audience
Afficher plus [+] Moins [-]anglais. Tremendous amounts of data generated from microbiome research studies during the last decades require not only standards for sampling and preparation of omics data but also clear concepts of how the metadata is prepared to ensure re-use for integrative and interdisciplinary microbiome analysis. Results In this Commentary, we present our views on the key issues related to the current system for metadata submission in omics research, and propose the development of a global metadata system. Such a system should be easy to use, clearly structured in a hierarchical way, and should be compatible with all existing microbiome data repositories, following common standards for minimal required information and common ontology. Although minimum metadata requirements are essential for microbiome datasets, the immense technological progress requires a flexible system, which will have to be constantly improved and re-thought. While FAIR principles (Findable, Accessible, Interoperable, and Reusable) are already considered, international legal issues on genetic resource and sequence sharing provided by the Convention on Biological Diversity need more awareness and engagement of the scientific community. The suggested approach for metadata entries would strongly improve retrieving and re-using data as demonstrated in several representative use cases. These integrative analyses, in turn, would further advance the potential of microbiome research for novel scientific discoveries and the development of microbiome-derived products.
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