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CETAF-DiSSCo/COVID19-TAF biodiversity-related knowledge hub working group: indexed biotic interactions and review summary

Poelen, Jorrit; Upham, Nathan; Agosti, Donat; Ruschel, Tatiana; Guidoti, Marcus; Reeder, DeeAnn; Simmons, Nancy; Penev, Lyubomir; Dimitrova, Mariya; Csorba, Gabor; Groom, Quentin; Willoughby, Anna


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{
  "publisher": "Zenodo", 
  "DOI": "10.5281/zenodo.3839098", 
  "language": "eng", 
  "title": "CETAF-DiSSCo/COVID19-TAF biodiversity-related knowledge hub working group: indexed biotic interactions and review summary", 
  "issued": {
    "date-parts": [
      [
        2020, 
        5, 
        22
      ]
    ]
  }, 
  "abstract": "<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>\n\n<p>This archive contains the biodiversity datasets of interest identified in period 14 April-21 May 2020 through COVID19-TAF activities and subsequently indexed by Global Biotic Interactions (GloBI, https://globalbioticinteractions.org).&nbsp; 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>\n\n<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>\n\n<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>\n\n<p>Funding:<br>\nThe creation of this archive was made possible in part by reporting software developed as part of the National Science Foundation award &quot;Collaborative Research: Digitization TCN: Digitizing collections to trace parasite-host associations and predict the spread of vector-borne disease,&quot; 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>\n\n<p>References:<br>\nJorrit 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>\n\n<p>GloBI Data Review Report</p>\n\n<p>Datasets under review:<br>\n&nbsp;- 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 2020-05-21T17:02:04.918Z<br>\n&nbsp;- De Rojas M, Do&ntilde;a 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 2020-05-21T17:02:09.381Z<br>\n&nbsp;- Pensoft Darwin Core Archives with associateTaxa columns accessed via https://github.com/globalbioticinteractions/pensoft-dwca/archive/a3e075e4d7a03ba3605af144e3f2a4e55e4bdb03.zip on 2020-05-21T17:02:17.674Z<br>\n&nbsp;- Pensoft Darwin Core Archives available via Integrated Publication Toolkit accessed via https://github.com/globalbioticinteractions/pensoft-ipt/archive/4ad4b47978324681289e36f8c2b247b1bcc97b1a.zip on 2020-05-21T17:02:45.806Z<br>\n&nbsp;- Olival, K. J., Hosseini, P. R., Zambrana-Torrelio, C., Ross, N., Bogich, T. L., &amp; Daszak, P. (2017). Host and viral traits predict zoonotic spillover from mammals. Nature, 546(7660), 646&ndash;650. doi:10.1038/nature22975 accessed via https://github.com/globalbioticinteractions/olival2017/archive/f61070a5339d0e6c6e76d7eb4e2102decb52317d.zip on 2020-05-21T17:02:48.553Z<br>\n&nbsp;- 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/bcfe5b7ada567771aedf291474c896dc94550681.zip on 2020-05-21T17:02:52.034Z<br>\n&nbsp;- Geiselman, Cullen K. and Tuli I. Defex. 2015. Bat Eco-Interactions Database. www.batplant.org accessed via https://github.com/globalbioticinteractions/batplant/archive/1fe61d1e90335cf3716365d1322c79abde5a4ca7.zip on 2020-05-21T17:11:53.998Z<br>\n&nbsp;- Eneida L. Hatcher, Sergey A. Zhdanov, Yiming Bao, Olga Blinkova, Eric P. Nawrocki, Yuri Ostapchuck, Alejandro A. Sch&auml;ffer, J. Rodney Brister, Virus Variation Resource &ndash; improved response to emergent viral outbreaks, Nucleic Acids Research, Volume 45, Issue D1, January 2017, Pages D482&ndash;D490, https://doi.org/10.1093/nar/gkw1065 . Data downloaded via https://www.ncbi.nlm.nih.gov/labs/virus/vssi on 2020-03-14 accessed via https://github.com/globalbioticinteractions/ncbi-virus/archive/60769efcda06b4719e358e3bae7bad93ccebabe6.zip on 2020-05-21T17:13:26.182Z<br>\n&nbsp;- Quentin J. Groom. 2020. Bat interation data manually extracted from literature. accessed via https://zenodo.org/record/3816676/files/qgroom/batinterations-v1.0.1.zip on 2020-05-22T02:13:51.699Z</p>\n\n<p>Generated on:<br>\n2020-05-22</p>\n\n<p>by:<br>\nGloBI&#39;s Elton 0.9.8<br>\n(see https://github.com/globalbioticinteractions/elton).</p>\n\n<p>Note that all files ending with .tsv are files formatted<br>\nas UTF8 encoded tab-separated values files.</p>\n\n<p>https://www.iana.org/assignments/media-types/text/tab-separated-values</p>\n\n<p><br>\nIncluded in this review archive are:</p>\n\n<p>README:<br>\n&nbsp; This file (lightly edited after initial automated generation).</p>\n\n<p>review_summary.tsv:<br>\n&nbsp; Summary across all reviewed collections of total number of distinct review comments.</p>\n\n<p>review_summary_by_collection.tsv:<br>\n&nbsp; Summary by reviewed collection of total number of distinct review comments.</p>\n\n<p>indexed_interactions_by_collection.tsv:<br>\n&nbsp; Summary of number of indexed interaction records by institutionCode and collectionCode.</p>\n\n<p>review_comments.tsv.gz:<br>\n&nbsp; All review comments by collection.</p>\n\n<p>indexed_interactions_full.tsv.gz:<br>\n&nbsp; All indexed interactions for all reviewed collections.</p>\n\n<p>indexed_interactions_simple.tsv.gz:<br>\n&nbsp; All indexed interactions for all reviewed collections selecting only sourceInstitutionCode, sourceCollectionCode, sourceCatalogNumber, sourceTaxonName, interactionTypeName and targetTaxonName.</p>\n\n<p>datasets_under_review.tsv:<br>\n&nbsp; Details on the datasets under review.</p>\n\n<p>elton.jar:<br>\n&nbsp; Program used to update datasets and generate the review reports and associated indexed interactions.</p>\n\n<p>datasets.zip:<br>\n&nbsp; source datasets collected by elton in process of executing the generate_report.sh script.</p>\n\n<p>generate_report.sh:<br>\n&nbsp; program used to generate the report</p>\n\n<p>generate_report.log:<br>\n&nbsp; log file generated as part of running the generate_report.sh script</p>", 
  "author": [
    {
      "family": "Poelen, Jorrit"
    }, 
    {
      "family": "Upham, Nathan"
    }, 
    {
      "family": "Agosti, Donat"
    }, 
    {
      "family": "Ruschel, Tatiana"
    }, 
    {
      "family": "Guidoti, Marcus"
    }, 
    {
      "family": "Reeder, DeeAnn"
    }, 
    {
      "family": "Simmons, Nancy"
    }, 
    {
      "family": "Penev, Lyubomir"
    }, 
    {
      "family": "Dimitrova, Mariya"
    }, 
    {
      "family": "Csorba, Gabor"
    }, 
    {
      "family": "Groom, Quentin"
    }, 
    {
      "family": "Willoughby, Anna"
    }
  ], 
  "version": "0.2", 
  "type": "dataset", 
  "id": "3839098"
}
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