Biodiversity Information Science and Standards :
Conference Abstract
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Corresponding author: Nathan S Upham (nathan.upham@asu.edu)
Received: 01 Oct 2020 | Published: 09 Oct 2020
© 2020 Nathan Upham, Donat Agosti, Jorrit Poelen, Lyubomir Penev, Deborah Paul, DeeAnn Reeder, Nancy B. Simmons, Gabor Csorba, Quentin Groom, Mariya Dimitrova, Joseph Miller
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Upham NS, Agosti D, Poelen J, Penev L, Paul D, Reeder DM, Simmons NB, Csorba G, Groom Q, Dimitrova M, Miller JT (2020) Liberating Biodiversity Data From COVID-19 Lockdown: Toward a knowledge hub for mammal host-virus information. Biodiversity Information Science and Standards 4: e59199. https://doi.org/10.3897/biss.4.59199
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A deep irony of COVID-19 likely originating from a bat-borne coronavirus (
Understanding why biodiversity science was unprepared—and how to fix it before the next pandemic—has been the focus of our COVID-19 Taskforce since April 2020 and is continuing (organized by CETAF and DiSSCo). We are a group of museum-based and academic scientists with the goal of opening the rich ecological data stored in natural history collections to the research public. This information is rooted in what may seem an unlikely location—taxonomic names and their historical usages, which are the keys for searching literature and extracting linked ecological data (Fig.
Taxonomic names and their usages are the key for unlocking host-virus interaction data. Flow of information from digitizing taxonomic treatments containing species names and their historical usages (Plazi and Zenodo), to searching biodiversity literature for data linked to names, to connecting those biotic interactions in an ecological network (GloBI). Data can also flow directly into GloBI from Pensoft-style journals that publish data with computer-readable tags.
Overall, considerable progress was made. In total, 85,492 new interactions were added to GloBI from 14 April to 21 May 2020 (see entire dataset on Zenodo:
We can liberate host-virus data from publications, but doing so is expensive and does not scale to the continued influx of new articles that are inadequately digitized. Our efforts make it clear that Pensoft-style semantic publishing should be expanded to all major journals. The pandemic has created an opportunity for re-thinking the way we do science in the digital age. Thankfully, our future is not the past, so we do not have to keep wasting resources to digitially 'rediscover' biodiversity knowledge. We collectively call for changes to the publishing paradigm, so that research findings are directly accessible, citable, discoverable, and reusable for creating complete forms of digital knowledge.
zoonotic disease risk, spillover, virus, mammal, bat, taxonomy, semantic publishing
Nathan S Upham
TDWG 2020