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CETAF-DiSSCo/COVID19-TAF biodiversity-related knowledge hub working group: indexed biotic interactions and review summary
<p>This data publication originated as part of developing a biodiversity-related knowledge hub on COVID-19 via COVID19-TAF - Communities Taking Action (https://cetaf.org/covid19-taf-communities-taking-action), a community-rooted initiative raised jointly by the Consortium of European Taxonomic Facilitaties (CETAF, https://cetaf.org) and Distributed Systems of Scientific Collections (DiSSCo, https://www.dissco.eu/).</p> <p>This archive contains the biodiversity datasets of interest identified in period 14 April-6 October 2020 through COVID19-TAF activities and subsequently indexed by Global Biotic Interactions (GloBI, https://globalbioticinteractions.org). GloBI provides open access to finding species interaction data (e.g., predator-prey, pollinator-plant, virus-host, parasite-host) by combining existing open datasets using open source software.</p> <p>These identified datasets (see references and reviews below) add to a growing collection of open species interaction datasets already indexed by GloBI. So, this data publication only includes a small subset of indexed datasets and include only datasets that were added as a direct consequence of COVID19-TAF activities of the biodiversity-related knowledge hub working group.</p> <p>If you have questions or comments about this publication, please open an issue at https://github.com/ParasiteTracker/tpt-reporting or contact the authors by email.</p> <p>Funding:<br> The creation of this archive was made possible in part by reporting software developed as part of the National Science Foundation award "Collaborative Research: Digitization TCN: Digitizing collections to trace parasite-host associations and predict the spread of vector-borne disease," Award numbers DBI:1901932 and DBI:1901926 . Also, this material is based upon work supported by the National Science Foundation under Grant No. DGE-1545433 .</p> <p>References:<br> Jorrit H. Poelen, James D. Simons and Chris J. Mungall. (2014). Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2014.08.005.</p> <p>GloBI Data Review Report</p> <p>Datasets under review:<br> - Geiselman, Cullen K. & Sarah Younger. 2020. Bat Eco-Interactions Database. www.batbase.org accessed via https://github.com/globalbioticinteractions/batbase/archive/9c65cfeee1a054f9db8cd8bf6892017fd1b3c840.zip on 2020-10-04T22:53:45.576Z<br> - Geiselman, Cullen K. and Tuli I. Defex. 2015. Bat Eco-Interactions Database. www.batplant.org accessed via https://github.com/globalbioticinteractions/batplant/archive/a2e1b57052244d5251d17e96ea61f58bea88975e.zip on 2020-10-04T22:54:28.727Z<br> - Daniel Becker, Gregory F Albery, Anna R Sjodin, Timothee Poisot, Tad Dallas, Evan A. Eskew, Maxwell J. Farrell, Sarah Guth, Barbara A Han, Nancy B Simmons, Colin J Carlson. 2020. Predicting wildlife hosts of betacoronaviruses for SARS-CoV-2 sampling prioritization. bioRxiv 2020.05.22.111344; doi: https://doi.org/10.1101/2020.05.22.111344 accessed via https://github.com/globalbioticinteractions/becker2020/archive/47c6ad28e1c5058f3c13ca69a59fdf21229e8d7f.zip on 2020-10-04T22:54:46.723Z<br> - Chen L, Liu B, Yang J, Jin Q, 2014. DBatVir: the database of bat-associated viruses. Database (Oxford). 2014:bau021. doi:10.1093/database/bau021 accessed via https://github.com/globalbioticinteractions/dbatvir/archive/a906d76e362484d3ca1edbe9683f672838ab70b0.zip on 2020-10-04T22:56:13.913Z<br> - Chen L, Liu B, Wu Z, Jin Q, Yang J, 2017. DRodVir: A resource for exploring the virome diversity in rodents. J Genet Genomics. 44(5):259-264. accessed via https://github.com/globalbioticinteractions/drodvir/archive/0346c0e8d4d66c6400e9965bd6a6aeed24cd7586.zip on 2020-10-04T23:06:04.368Z<br> - Agosti, Donat. 2020. Transcription of Linné, C. von, 1758. Systema naturae per regna tria naturae secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Available at: http://dx.doi.org/10.5962/bhl.title.542 . accessed via https://github.com/globalbioticinteractions/linnaeus1758/archive/a818060080fa04a88dac6df1ae5b897304ae8877.zip on 2020-10-05T00:46:04.852Z<br> - Mollentze, Nardus, & Streicker, Daniel G. (2019). Viral zoonotic risk is homogenous among taxonomic orders of mammalian and avian reservoir hosts (Version 1.0.0) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.3516613 accessed via https://github.com/globalbioticinteractions/mollentze2019/archive/ad12dc74d03c3d992618f16c37cafb7f7ffd9d01.zip on 2020-10-05T00:50:55.878Z<br> - Eneida L. Hatcher, Sergey A. Zhdanov, Yiming Bao, Olga Blinkova, Eric P. Nawrocki, Yuri Ostapchuck, Alejandro A. Schäffer, J. Rodney Brister, Virus Variation Resource – improved response to emergent viral outbreaks, Nucleic Acids Research, Volume 45, Issue D1, January 2017, Pages D482–D490, https://doi.org/10.1093/nar/gkw1065 . accessed via https://github.com/globalbioticinteractions/ncbi-virus/archive/531a8d743d7adcf1153a19087e5d3c5b76750e3e.zip on 2020-10-05T00:53:53.646Z<br> - Olival, K. J., Hosseini, P. R., Zambrana-Torrelio, C., Ross, N., Bogich, T. L., & Daszak, P. (2017). Host and viral traits predict zoonotic spillover from mammals. Nature, 546(7660), 646–650. doi:10.1038/nature22975 accessed via https://github.com/globalbioticinteractions/olival2017/archive/f61070a5339d0e6c6e76d7eb4e2102decb52317d.zip on 2020-10-05T00:56:43.356Z<br> - Pensoft Darwin Core Archives with associateTaxa columns accessed via https://github.com/globalbioticinteractions/pensoft-dwca/archive/ee8831a2a391203f4fa8c05a0ddd927202b234bf.zip on 2020-10-05T00:56:51.868Z<br> - Pensoft Darwin Core Archives available via Integrated Publication Toolkit accessed via https://github.com/globalbioticinteractions/pensoft-ipt/archive/4ad4b47978324681289e36f8c2b247b1bcc97b1a.zip on 2020-10-05T00:58:01.912Z<br> - De Rojas M, Doña J, Dimov I (2020) A comprehensive survey of Rhinonyssid mites (Mesostigmata: Rhinonyssidae) in Northwest Russia: New mite-host associations and prevalence data. Biodiversity Data Journal 8: e49535. https://doi.org/10.3897/BDJ.8.e49535 accessed via https://github.com/globalbioticinteractions/pensoft-table/archive/3488e0397ca4e083d5eca6949951e426a75713e3.zip on 2020-10-05T00:58:03.647Z<br> - Marcus Guidoti, Tatiana Ruschel, Donat Agosti. 2020. Corona virus related biotic associations manually extracted from literature. Plazi. accessed via https://github.com/globalbioticinteractions/plazi-covid19/archive/326578b0d9f974760dcd2e962d86636a6487a6c0.zip on 2020-10-05T00:58:08.025Z<br> - Shaw, LP, Wang, AD, Dylus, D, et al. The phylogenetic range of bacterial and viral pathogens of vertebrates. Mol Ecol. 2020; 29: 3361– 3379. https://doi.org/10.1111/mec.15463 accessed via https://github.com/globalbioticinteractions/shaw2020/archive/bb9ab857b7fdbb4e931752d01b43d37b3ada77cf.zip on 2020-10-05T01:05:23.554Z<br> - OpenBiodiv. 2020. Annotated biotic interaction tables from Pensoft publications. accessed via https://github.com/pensoft/pensoft-interaction-tables/archive/bb7d1dc9f2eba220a61502e06e6114053fd30788.zip on 2020-10-05T03:03:23.372Z<br> - Quentin J. Groom. 2020. Bat interation data manually extracted from literature. accessed via https://github.com/qgroom/batinterations/archive/70108945f9014aa0ac1db920191867f7e151c793.zip on 2020-10-05T03:04:11.533Z</p> <p>Generated on:<br> 2020-10-06</p> <p>by:<br> GloBI's Elton 0.10.2<br> (see https://github.com/globalbioticinteractions/elton).</p> <p> </p> <p>Note that all files ending with .tsv are files formatted<br> as UTF8 encoded tab-separated values files.</p> <p>https://www.iana.org/assignments/media-types/text/tab-separated-values</p> <p><br> Included in this review archive are:</p> <p>README:<br> This file.</p> <p>review_summary.tsv:<br> Summary across all reviewed collections of total number of distinct review comments.</p> <p>review_summary_by_collection.tsv:<br> Summary by reviewed collection of total number of distinct review comments.</p> <p>indexed_interactions_by_collection.tsv:<br> Summary of number of indexed interaction records by institutionCode and collectionCode.</p> <p>review_comments.tsv.gz:<br> All review comments by collection.</p> <p>indexed_interactions_full.tsv.gz:<br> All indexed interactions for all reviewed collections.</p> <p>indexed_interactions_simple.tsv.gz:<br> All indexed interactions for all reviewed collections selecting only sourceInstitutionCode, sourceCollectionCode, sourceCatalogNumber, sourceTaxonName, interactionTypeName and targetTaxonName.</p> <p>datasets_under_review.tsv:<br> Details on the datasets under review.</p> <p>elton.jar:<br> Program used to update datasets and generate the review reports and associated indexed interactions.</p> <p><br> datasets.zip:<br> source datasets collected by elton in process of executing the generate_report.sh script.</p> <p>generate_report.sh:<br> program used to generate the report</p> <p>generate_report.log:<br> log file generated as part of running the generate_report.sh script</p>
Supplementary material 1 from: Koureas D, Livermore L, Addink W, Alonso E, Alonso JM, Casino A, Dusoulier F, Ferreira V, Grieb J, Groom Q, Islam S, Kõljalg U, Lymer G, Marhold K, Paleco C, Pijls S, Scory S, Scott B, Weiland C, Worley K (2024) DiSSCo Transition Abridged Grant Proposal. Research Ideas and Outcomes 10: e118241. https://doi.org/10.3897/rio.10.e118241
Letter of Intent for Collaboration: Development of a Global Partnership on Persistent Identification of Digital Extended Specimens & other Natural Science Collections Data Entities
Supplementary material 3 from: Hardisty AR, Addink W, Glöckler F, Güntsch A, Islam S, Weiland C (2021) A choice of persistent identifier schemes for the Distributed System of Scientific Collections (DiSSCo). Research Ideas and Outcomes 7: e67379. https://doi.org/10.3897/rio.7.e67379
Comparison of main roles and responsibilities in the two main categories of administration of a Handle-based PID scheme
DiSSCo Partner Capabilities Survey 2017
<p>Survey carried out among the DiSSCo consortium partners to have insight in the partner capabilities, in preparation for the ESFRI Hearing held early 2018. Contains raw plus corrected data.</p>
Supplementary material 4 from: Hardisty A, Livermore L, Walton S, Woodburn M, Hardy H (2020) Costbook of the digitisation infrastructure of DiSSCo. Research Ideas and Outcomes 6: e58915. https://doi.org/10.3897/rio.6.e58915
Cost Books - Original Responses
Supplementary material 5 from: Hardisty A, Livermore L, Walton S, Woodburn M, Hardy H (2020) Costbook of the digitisation infrastructure of DiSSCo. Research Ideas and Outcomes 6: e58915. https://doi.org/10.3897/rio.6.e58915
Cost books - RBINS
Supplementary material 3 from: Hardisty A, Livermore L, Walton S, Woodburn M, Hardy H (2020) Costbook of the digitisation infrastructure of DiSSCo. Research Ideas and Outcomes 6: e58915. https://doi.org/10.3897/rio.6.e58915
Cost Books - Flattened Data
Figure 6 from: Hardisty A, Livermore L, Walton S, Woodburn M, Hardy H (2020) Costbook of the digitisation infrastructure of DiSSCo. Research Ideas and Outcomes 6: e58915. https://doi.org/10.3897/rio.6.e58915
Figure 6 Returned costbooks versus stated capability to digitise from Cocks et al. (2020). Legend: Graded shaded = stated capability to digitise. Black tickbox = completed costbook returned for that category. RBGK 'Other' = fungi collection. MNHN 'Herbarium sheets' = two workflows (day-to-day digitisation in the museum, and Recolnat project workflow). MNHN 'Other' = marine invertebrates collection. UTARTU 'Other' = lichens and fungi. NHMUK 'Pinned insects' = two workflows (standard workflow with label removal, and ALICE workflow with label remaining in situ).
Supplementary material 1 from: Hardisty A, Livermore L, Walton S, Woodburn M, Hardy H (2020) Costbook of the digitisation infrastructure of DiSSCo. Research Ideas and Outcomes 6: e58915. https://doi.org/10.3897/rio.6.e58915
Cost Template Data Extraction Script
Supplementary material 2 from: Hardisty A, Livermore L, Walton S, Woodburn M, Hardy H (2020) Costbook of the digitisation infrastructure of DiSSCo. Research Ideas and Outcomes 6: e58915. https://doi.org/10.3897/rio.6.e58915
Costbook Template
FAIR Digital Object and DiSSCo Research Infrastructure Design
<p>This presentation is about how <a href="https://dissco.eu">DiSSCo</a> (Distributed System of Scientific Collections) is using the FAIR Digital Object as the cornerstone of a research infrastructure design. DiSSCo -- a new Research Infrastructure currently in the preparation phase -- will digitally unify European natural science assets under common curation and access and will ensure that data is Findable, Accessible, Interoperable and Reusable (FAIR). DiSSCo will integrate a fragmented landscape of natural science collections, transforming it into a unified, robust, quality ensured knowledge base of unprecedented scale for bio- and geodiversity.</p> <p>With a brief historical context of FAIR Digital Object, this presentation introduces the concept of Digital Specimen. Then it highlights the incorporation of outputs from several <a href="https://rd-alliance.org/">RDA</a> (Research Data Alliance) interests and working groups in the design decision.</p>
Figure 2 from: Raes N, Casino A, Goodson H, Islam S, Koureas D, Schiller EK, Schulman L, Tilley L, Robertson T (2020) White paper on the alignment and interoperability between the Distributed System of Scientific Collections (DiSSCo) and EU infrastructures - The case of the European Environment Agency (EEA). Research Ideas and Outcomes 6: e62361. https://doi.org/10.3897/rio.6.e62361
Figure 2 The current and required implementation readiness levels for DiSSCo to enter the construction phase of the DiSSCo RI. The grey arrows indicate the tasks for the DiSSCo Prepare project.
Figure 3 from: Raes N, Casino A, Goodson H, Islam S, Koureas D, Schiller EK, Schulman L, Tilley L, Robertson T (2020) White paper on the alignment and interoperability between the Distributed System of Scientific Collections (DiSSCo) and EU infrastructures - The case of the European Environment Agency (EEA). Research Ideas and Outcomes 6: e62361. https://doi.org/10.3897/rio.6.e62361
Figure 3 An example of a simple Digital Specimen (Hardisty 2020). Arrows point to identifiers of linked information that was derived from or is related to the physical specimen it represents. dissco.tech blog post.
Figure 4 from: Raes N, Casino A, Goodson H, Islam S, Koureas D, Schiller EK, Schulman L, Tilley L, Robertson T (2020) White paper on the alignment and interoperability between the Distributed System of Scientific Collections (DiSSCo) and EU infrastructures - The case of the European Environment Agency (EEA). Research Ideas and Outcomes 6: e62361. https://doi.org/10.3897/rio.6.e62361
Figure 4 The links and interactions between the EEA, ETCs (European Topic Centres), NFPs (National Focal Points), and NRCs (National Reference Centres) - image from EEA website*25.
Supplementary material 1 from: Lymer G, Leliaert F, Mergen P, Pijls S (2023) Pre-Commercial Procurement framework and European funding sources for European Research Infrastructure Consortiums: Insights from the DiSSCo ERIC development. Research Ideas and Outcomes 9: e113294. https://doi.org/10.3897/rio.9.e113294
Glossary
Supplementary material 2 from: Lymer G, Leliaert F, Mergen P, Pijls S (2023) Pre-Commercial Procurement framework and European funding sources for European Research Infrastructure Consortiums: Insights from the DiSSCo ERIC development. Research Ideas and Outcomes 9: e113294. https://doi.org/10.3897/rio.9.e113294
ANNEXE 1: Additional and non-EU funding sources
Figure 3 from: Koureas D, Livermore L, Addink W, Alonso E, Alonso JM, Casino A, Dusoulier F, Ferreira V, Grieb J, Groom Q, Islam S, Kõljalg U, Lymer G, Marhold K, Paleco C, Pijls S, Scory S, Scott B, Weiland C, Worley K (2024) DiSSCo Transition Abridged Grant Proposal. Research Ideas and Outcomes 10: e118241. https://doi.org/10.3897/rio.10.e118241
Figure 3 A schematic representation of the contributions of the DiSSCo Prepare and DiSSCo Transition Projects towards the optimum level of maturity across all required dimensions for the early-phase implementation of the RI.
Figure 6 from: Koureas D, Livermore L, Addink W, Alonso E, Alonso JM, Casino A, Dusoulier F, Ferreira V, Grieb J, Groom Q, Islam S, Kõljalg U, Lymer G, Marhold K, Paleco C, Pijls S, Scory S, Scott B, Weiland C, Worley K (2024) DiSSCo Transition Abridged Grant Proposal. Research Ideas and Outcomes 10: e118241. https://doi.org/10.3897/rio.10.e118241
Figure 6 Overview of the DiSSCo Data Infrastructure with core infrastructure (DSarch) and end-user service components.
Figure 2 from: Koureas D, Livermore L, Addink W, Alonso E, Alonso JM, Casino A, Dusoulier F, Ferreira V, Grieb J, Groom Q, Islam S, Kõljalg U, Lymer G, Marhold K, Paleco C, Pijls S, Scory S, Scott B, Weiland C, Worley K (2024) DiSSCo Transition Abridged Grant Proposal. Research Ideas and Outcomes 10: e118241. https://doi.org/10.3897/rio.10.e118241
Figure 2 Timeline of DiSSCo development until its implementation (Construction) phase through its new legal entity (ERIC). The Project acts as the bridge between DiSSCo Prepare and the start of the Construction (Implementation) Phase of the ERIC.
Figure 1 from: Koureas D, Livermore L, Addink W, Alonso E, Alonso JM, Casino A, Dusoulier F, Ferreira V, Grieb J, Groom Q, Islam S, Kõljalg U, Lymer G, Marhold K, Paleco C, Pijls S, Scory S, Scott B, Weiland C, Worley K (2024) DiSSCo Transition Abridged Grant Proposal. Research Ideas and Outcomes 10: e118241. https://doi.org/10.3897/rio.10.e118241
Figure 1 Conceptual approach to delivering a distributed infrastructure for European natural science collections.
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