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FAIR enough? A perspective on the status of nucleotide sequence data and metadata on public archives

View ORCID ProfileChristiane Hassenrück, Tobias Poprick, View ORCID ProfileVéronique Helfer, View ORCID ProfileMassimiliano Molari, View ORCID ProfileRaissa Meyer, View ORCID ProfileIvaylo Kostadinov
doi: https://doi.org/10.1101/2021.09.23.461561
Christiane Hassenrück
1Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Seestrasse 15, 18119 Rostock-Warnemünde, Germany
2MARUM - Center for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, 28359 Bremen, Germany
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  • For correspondence: christiane.hassenrueck@io-warnemuende.de
Tobias Poprick
3Leibniz Centre for Tropical Marine Research (ZMT), Fahrenheitstrasse 6, 28359 Bremen, Germany
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Véronique Helfer
3Leibniz Centre for Tropical Marine Research (ZMT), Fahrenheitstrasse 6, 28359 Bremen, Germany
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Massimiliano Molari
4Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359 Bremen, Germany
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Raissa Meyer
5Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
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Ivaylo Kostadinov
6GFBio - Gesellschaft für Biologische Daten e.V., c/o Research II, Campus Ring 1, 28759 Bremen, Germany
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Abstract

Knowledge derived from nucleotide sequence data is increasing in importance in the life sciences, as well as decision making (mainly in biodiversity policy). Metadata standards have been established to facilitate sustainable sequence data management according to the FAIR principles (Findability, Accessibility, Interoperability, Reusability). Here, we review the status of metadata available for raw read Illumina amplicon and whole genome shotgun sequencing data derived from ecological metagenomic material that are accessible at the European Nucleotide Archive (ENA), as well as the compliance of the primary sequence data (fastq files) with data submission requirements. While overall basic metadata, such as geographic coordinates, were retrievable in 98% of the cases for this type of sequence data, interoperability was not always ensured and other (mainly conditionally) mandatory parameters were often not provided at all. Metadata standards, such as the ‘Minimum Information about any(x) Sequence (MIxS)’, were only infrequently used despite a demonstrated positive impact on metadata quality. Furthermore, the sequence data itself did not meet the prescribed requirements in 31 out of 39 studies that were manually inspected. To tackle the most immediate needs to improve FAIR sequence data management, we provide a list of minimal suggestions to researchers, research institutions, funding agencies, reviewers, publishers, and databases, that we believe might have a potentially large positive impact on sequence data and metadata FAIRness, which is crucial for further research and its derived applications.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/chassenr/ENA-metadata

  • 5 https://www.tdwg.org/community/gbwg/MIxS/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted September 24, 2021.
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FAIR enough? A perspective on the status of nucleotide sequence data and metadata on public archives
Christiane Hassenrück, Tobias Poprick, Véronique Helfer, Massimiliano Molari, Raissa Meyer, Ivaylo Kostadinov
bioRxiv 2021.09.23.461561; doi: https://doi.org/10.1101/2021.09.23.461561
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FAIR enough? A perspective on the status of nucleotide sequence data and metadata on public archives
Christiane Hassenrück, Tobias Poprick, Véronique Helfer, Massimiliano Molari, Raissa Meyer, Ivaylo Kostadinov
bioRxiv 2021.09.23.461561; doi: https://doi.org/10.1101/2021.09.23.461561

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