The bioinformatics landscape in environmental omics: Lessons from a national ELIXIR survey

Summary

As a research infrastructure with a mission to provide services for bioinformatics, ELIXIR aims to identify and inform its target audiences. Here, we present a survey on a community of researchers studying the environment with omics approaches in Greece, one of the youngest member countries of ELIXIR. Personal interviews followed by quantitative and qualitative analysis were employed to document interactions and practices of the community and to perform a gap analysis for the transition toward multiomics and systems biology. Environmental omics in Greece mostly concerns production of data, in large majority on microbes and non-model organisms. Our survey highlighted (1) the popularity and suitability of targeted hands-on training events; (2) data quality and management issues as important elements for the transition to multiomics, and (3) lack of knowledge and misconceptions regarding interoperability, metadata standards, and pre-registration. The publicly available collected answers represent a valuable resource in view of future strategic planning.

Graphical abstract

Highlights

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  A national survey on environmental omics was performed at the ELIXIR-GR kick-start

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  The research community shows medium bioinformatics and FAIR literacy

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  Researchers primarily study non-model organisms by producing (meta-) genomic data

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  Practical training can help addressing multiomics challenges and expertise gaps

Abstract

Environmental biotechnology; Bioinformatics; Omics