Biodiversity and why it needs better data archiving

Shenade Annie Kerketta, Amity University Kolkata

Biodiversity is known as the collection of life on Earth at all levels. It covers everything, from genes to ecosystems. In short, biodiversity not only covers rare species but all life forms. Biodiversity is important to restore the balance on Earth. Biodiversity is also important as it provides us with a lot of things. However, it has its rights as well. In terms of utilitarian values, biodiversity provides us with food, shelter, medicine, fuels, etc. Along with that it also provides crucial services such as nutrient cycling, pollination, climate regulation, water filtration, etc. It is needless to say that there can be many more positive values still which are not yet recognized.

The Study:

Recently, a group of scientists has done a study to make it more useful to humankind. These scientists tried to find out whether the genomic data and spatiotemporal metadata were adequately archived. Metadata is essentially the information regarding your data. While studying, scientists pointed out a huge flaw in genomic datasets. The spatiotemporal metadata needed for those genomic datasets was lacking in 86% of the cases. As spatiotemporal metadata is necessary for genetic biodiversity surveillance, this lack of information can cause a lot of problems.

Nowadays the genomic datasets are becoming more and more available. So much so that researchers can virtually replicate the whole genome from any species. Naturally, these genomic data once archived have an immense reuse value for measuring genetic diversity. But to reuse these genomic data, one must know about the spatiotemporal context of the sample. Without that information, the genetic data will have a much smaller effect on genetic biodiversity surveillance.

This drives the scientists to conduct a structured search of publicly available data. INSDC (International Nucleotide Sequence Database Collaboration) is the leading repository of raw genomic data. Most journal authors are required to archive their genetic data in INSDC. After accessing the INSDC database researchers focused on the most common targets for biodiversity studies. Which are wild and domesticated species. Upon acquiring 5043 datasets from 327577 individual organisms, only 14% were seen to have included the spatiotemporal metadata. After removing domesticated species, 233639 sequenced individuals from 3903 datasets were left. Among which only 17% and 41% had geospatial coordinates and collection year respectively as 14% had both.

Findings:

1. To investigate to recover spatiotemporal metadata manually 848 genomic datasets were prioritized. After putting manual labours individuals in 63% and 40% had had geospatial coordinates respectively as 33% had both.
2. Even after putting in manual labour only a part of the study was successful. This shows that working directly with the authors is the only strategy to recover spatiotemporal metadata. However, with time even that is bound to be difficult.
3. In those cases where the metadata was not collected or lost, the recovery is impossible.

Conclusion:

The silver lining here is that from 2008 the metadata information was to some extent recorded. The solution to this problem is the understanding of why metadata is essential. Without valid metadata the study conducted becomes nonessential. Which in return hinders further studies. The SRA (Sequence Read Archive) grew by 50% in 2019 only. In the meantime, 35000 species are now endangered as the sixth mass extinction is underway. It is high time to reduce this metadata gap. Otherwise, future studies and experiments are bound to face some serious problems.

Also read: LexExp: A System to expand lexicons for noisy biomedical texts

Reference: Toczydlowski, R. H., Liggins, L., Gaither, M. R., Anderson, T. J., Barton, R. L., Berg, J. T., Beskid, S. G., Davis, B., Delgado, A., Farrell, E., Ghoojaei, M., Himmelsbach, N., Holmes, A. E., Queeno, S. R., Trinh, T., Weyand, C. A., Bradburd, G. S., Riginos, C., Toonen, R. J., & Crandall, E. D. (2021). Poor data stewardship will hinder global genetic diversity surveillance. Proceedings of the National Academy of Sciences, 118(34), e2107934118. https://doi.org/10.1073/pnas.2107934118

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