This page includes links, meeting info and timelines of activities related to developing research questions and supporting data products in context of COVID-19. These activities were initiated via COVID19-TAF - Communities Taking Action, a community-rooted initiative raised jointly by CETAF and DiSSCo.

The information on this page does not aim to be a complete overview of activities, but rather a minimalist collection of past accomplishments and ongoing activities.

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publications / grants

Contact Info

Integrations

GloBI<–>Pensoft and GloBI<–>Plazi/Zenodo integrations originated from these COVID-19 activities. Please visit respective integration pages here and here to see their status.

Timeline

22 May 2020 - Released data publication: Poelen, Jorrit, Upham, Nathan, Agosti, Donat, Ruschel, Tatiana, Guidoti, Marcus, Reeder, DeeAnn, … Willoughby, Anna. (2020). CETAF-DiSSCo/COVID19-TAF biodiversity-related knowledge hub working group: indexed biotic interactions and review summary (Version 0.2) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.3839098 .

26 May 2020 - Quentin published blog post “Releasing Biological Data from COVID-19 Lockdown” at https://www.globalbioticinteractions.org/2020/05/26/releasing-biological-data-from-COVID-19-lockdown/

16 July 2020 - Guido adds Plazi-mediated publications to Zenodo using the custom “host of” Zenodo annotation that Alex implemented (e.g., Luo et al. 2018). Soon after, Jorrit enabled the indexing of these Zenodo pubs. For context, see related github issue and related tweets by Donat and GloBI .

16 July 2020 - CETAF published short video introduction of some COVID-19 knowledge hub contributors

17 July 2020 - video recording of ~10 minute overview of outcomes by Nathan titled “Liberating biodiversity data from Covid-19 lockdown” as part of the CETAF-DiSSCo COVID-19 TaF Public event .

17 July 2020 - Mariya published blog post “Pensoft – GloBI workflow for FAIR data exchange and indexing of biotic interactions locked within scholarly articles” at https://blog.pensoft.net/2020/07/17/pensoft-globi-workflow-for-fair-data-exchange-and-indexing-of-biotic-interactions-locked-within-scholarly-articles/.

17 July 2020 - Donat published a blog post “Time for an interim review of Plazi’s Covid-19 related activities” at http://plazi.org/news/beitrag/time-for-an-interim-review-of-plazis-covid-19-related-activities/3e26b3bc95a4b39f0a2a9d7fccee8b19/.

11 Aug 2020 - Mariya submitted abstract “Semantic Publishing Enables Text Mining of Biotic Interactions” to virtual TDWG 2020 annual conference Oct 19-23 2020.

12 Aug 2020 - Nathan submitted abstract “Liberating Biodiversity Data From COVID-19 Lockdown: Toward a knowledge hub for mammal host-virus information” to virtual TDWG 2020 annual conference Oct 19-23 2020.

6 Oct 2020 - Released data publication: Poelen, Jorrit, Upham, Nathan, Agosti, Donat, Ruschel, Tatiana, Guidoti, Marcus, Reeder, DeeAnn, Simmons, Nancy; Penev, Lyubomir; Dimitrova, Mariya; Csorba, Gabor; Groom, Quentin; Willoughby, Anna. (2020). CETAF-DiSSCo/COVID19-TAF biodiversity-related knowledge hub working group: indexed biotic interactions and review summary (Version 0.3) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4068958 .

23 Oct 2020 - Nathan Upham presents on at TDWG 2020 Conference: 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. Presentation slides at: https://drive.google.com/file/d/17m976m-hO_c6IjmLHd6DPa8CR7gS7ycq/ .

12 Nov 2020 - Donat Agosti presents at RDA’s 2020 Meeting : Agosti, Donat, Poelen, Jorrit, Ioannidis, Alex, & Guidoti, Marcus. (2020, November). CETAF-DiSSCo COVID-19 TaF results in publishing biotic interactions. Presented at the RDA’s 16th Plenary Meeting (RDA P16), Zenodo. http://doi.org/10.5281/zenodo.4269959 .

15 June 2021 - publication of: Groom Q, Adriaens T, Bertolino S, Phelps K, Poelen JH, Reeder DM, Richardson DM, Simmons NB, Upham N (2021) Holistic understanding of contemporary ecosystems requires integration of data on domesticated, captive and cultivated organisms . Biodiversity Data Journal 9: e65371. doi:10.3897/BDJ.9.e65371.

21 June 2021 - Nathan Upham (PI) and DeeAnn Reeder (Co-PI) et al. awarded NIH grant “Intelligently predicting viral spillover risks from bats and other wild mammals” Project number 1R21AI164268-01 See also https://reporter.nih.gov/project-details/10289637 .

23 Sept 2021 - publication of: Van der Jeucht L, Groom Q, Agosti D, Phelps K, Reeder DM, Simmons NB (2021) Using iNaturalist to monitor adherence to best practices in bat handling. Biodiversity Data Journal 9: e68052. https://doi.org/10.3897/BDJ.9.e68052

23 Sept 2021 - publication of: Nathan S Upham, Jorrit H Poelen, Deborah Paul, Quentin J Groom, Nancy B Simmons, Maarten P M Vanhove, Sandro Bertolino, DeeAnn M Reeder, Cristiane Bastos-Silveira, Atriya Sen, Beckett Sterner, Nico M Franz, Marcus Guidoti, Lyubomir Penev, Donat Agosti (2021) Liberating host–virus knowledge from biological dark data. The Lancet Planetary Health. https://doi.org/10.1016/S2542-5196(21)00196-0.

7 Aug 2022 - publication of: Sherman, Aja C., Geiselman, Cullen, Simons, Nancy B., Upham, Nathan S., Poelen, Jorrit H., Reeder, DeeAnn M., Bertolino, Sandro, Groom, Quentin, Phelps, Kendra, Agosti, Donat, & Willoughby, Anna R. (2022, August 7). What do we not know? Quantifying data gaps and biases in knowledge of bat co-roosting. 19the International Bat Research Conference, Austin, Texas, USA. Zenodo. https://doi.org/10.5281/zenodo.6959687 . Note that Cullen Geiselman presented live at conference, and Aja C. Sherman recorded presentation narrative in accompanying mp4 for asynchronous viewing. pdf mp4 streaming video.

Publications

Peer-Review Publications

Cook, J. A., Arai, S., Armién, B., Bates, J., Bonilla, C. A. C., Cortez, M. B. de S., Dunnum, J. L., Ferguson, A. W., Johnson, K. M., Khan, F. A. A., Paul, D. L., Reeder, D. M., Revelez, M. A., Simmons, N. B., Thiers, B. M., Thompson, C. W., Upham, N. S., Vanhove, M. P. M., Webala, P. W., … Soltis, P. S. (2020). Integrating Biodiversity Infrastructure into Pathogen Discovery and Mitigation of Emerging Infectious Diseases. BioScience, 70(7), 531–534. https://doi.org/10.1093/biosci/biaa064

Upham, N. S., Poelen, J. H., Paul, D., Groom, Q. J., Simmons, N. B., Vanhove, M. P. M., Bertolino, S., Reeder, D. M., Bastos-Silveira, C., Sen, A., Sterner, B., Franz, N. M., Guidoti, M., Penev, L., & Agosti, D. (2021). Liberating host–virus knowledge from biological dark data. The Lancet Planetary Health, 0(0). https://doi.org/10.1016/S2542-5196(21)00196-0

Groom, Q., Adriaens, T., Bertolino, S., Phelps, K., Poelen, J., Reeder, D., Richardson, D., Simmons, N., Trekels, M., & Upham, N. (2022). The Importance of Collecting and Archiving Data on Domestic and Cultivated Organisms. Biodiversity Information Science and Standards, 6, e90864. https://doi.org/10.3897/biss.6.90864

Groom, Q., Adriaens, T., Bertolino, S., Phelps, K., Poelen, J., Reeder, D., Richardson, D., Simmons, N., & Upham, N. (2021). Holistic understanding of contemporary ecosystems requires integration of data on domesticated, captive and cultivated organisms. Biodiversity Data Journal, 9, e65371. https://doi.org/10.3897/BDJ.9.e65371

Upham, N., Agosti, D., Poelen, J., Penev, L., Paul, D., Reeder, D., Simmons, N. B., Csorba, G., Groom, Q., Dimitrova, M., & Miller, J. (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

Van der Jeucht L, Groom Q, Agosti D, Phelps K, Reeder DM, Simmons NB (2021) Using iNaturalist to monitor adherence to best practices in bat handling. Biodiversity Data Journal 9: e68052. https://doi.org/10.3897/BDJ.9.e68052

Data Publications

Poelen, J., Upham, N., Agosti, D., Ruschel, T., Guidoti, M., Reeder, D., Simmons, N., Penev, L., Dimitrova, M., Csorba, G., Groom, Q., & Willoughby, A. (2020). CETAF-DiSSCo/COVID19-TAF biodiversity-related knowledge hub working group: Indexed biotic interactions and review summary [Data set]. Zenodo. https://doi.org/10.5281/zenodo.4068958

Mast, A. R., Paul, D. L., Rios, N., Krimmel, E. R., Bruhn, R., Shorthouse, D. P., Simmons, N. B., Upham, N., & Soltis, P. (2020). Rapid Creation of a Data Product for the World’s Specimens of Horseshoe Bats and Relatives, a Known Reservoir for Coronaviruses [Data set]. Zenodo. https://doi.org/10.5281/zenodo.4047200

Presentations

Sherman, Aja C., Geiselman, Cullen, Simons, Nancy B., Upham, Nathan S., Poelen, Jorrit H., Reeder, DeeAnn M., Bertolino, Sandro, Groom, Quentin, Phelps, Kendra, Agosti, Donat, & Willoughby, Anna R. (2022, August 7). What do we not know? Quantifying data gaps and biases in knowledge of bat co-roosting. 19th International Bat Research Conference, Austin, Texas, USA. Zenodo. https://doi.org/10.5281/zenodo.6959687

Grants

U.S. National Institutes of Health, “Intelligently predicting viral spillover risks from bats and other wild mammals” R21 in response to PA-19-068, Secondary Analysis of Existing Datasets for Advancing Infectious Disease Research (PIs N. Upham and D. Reeder; also B. Sterner, A. Sen, N. Franz, A. Varsani, J. Rees, D. Agosti, J. Poelen). Awarded: $301,232 direct costs (2021-2023), 1R21AI164268-01.

U.S. National Science Foundation, “RAPID: Rapid Creation of a Data Product for the World’s Specimens of Horseshoe Bats and Relatives, a Known Reservoir for Coronaviruses” PI A. Mast, Co-PIs N. Rios, D. Paul https://www.nsf.gov/awardsearch/showAward?AWD_ID=2033973