Metadata harmonization–Standards are the key for a better usage of omics data for integrative microbiome analysis

Abstract

Background 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. Conclusions 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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“…Consequently, several researchers opt to furnish only the bare minimum of requisite data, or employ inaccurate terminology when describing their experimental data.These aspects hinder the aggregation of findings through integrative analyses. What we know is that standards are the key to a better usage of omics data for integrative microbiome analysis (Cernava et al 2022) and, at the same time, users require a system that should be easy to use, clearly structured in a hierarchical way, and should be compatible with existing data repositories. Regarding nucleotide sequence data storage, three are the main databases: the Sequence Read Archive (SRA) maintained by the National Center for Biotechnology Information (NCBI) (Kodama et al 2012), the European Nucleotide Archive (ENA) operated by the European Bioinformatics Institute (EBI) (Leinonen et al 2011), and the Sequence Read Archive (DRA) administered by the DNA Data Bank of Japan (DDBJ) (Mashima et al 2017).…”