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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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  <identifier identifierType="DOI">10.5281/zenodo.3839098</identifier>
  <creators>
    <creator>
      <creatorName>Poelen, Jorrit</creatorName>
      <givenName>Jorrit</givenName>
      <familyName>Poelen</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-3138-4118</nameIdentifier>
      <affiliation>Ronin Institute</affiliation>
    </creator>
    <creator>
      <creatorName>Upham, Nathan</creatorName>
      <givenName>Nathan</givenName>
      <familyName>Upham</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-5412-9342</nameIdentifier>
      <affiliation>Arizona State University</affiliation>
    </creator>
    <creator>
      <creatorName>Agosti, Donat</creatorName>
      <givenName>Donat</givenName>
      <familyName>Agosti</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-9286-1200</nameIdentifier>
      <affiliation>Plazi</affiliation>
    </creator>
    <creator>
      <creatorName>Ruschel, Tatiana</creatorName>
      <givenName>Tatiana</givenName>
      <familyName>Ruschel</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-9052-1760</nameIdentifier>
    </creator>
    <creator>
      <creatorName>Guidoti, Marcus</creatorName>
      <givenName>Marcus</givenName>
      <familyName>Guidoti</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-1744-6191</nameIdentifier>
    </creator>
    <creator>
      <creatorName>Reeder, DeeAnn</creatorName>
      <givenName>DeeAnn</givenName>
      <familyName>Reeder</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-8651-2012</nameIdentifier>
      <affiliation>Bucknell University</affiliation>
    </creator>
    <creator>
      <creatorName>Simmons, Nancy</creatorName>
      <givenName>Nancy</givenName>
      <familyName>Simmons</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-8807-7499</nameIdentifier>
      <affiliation>American Museum of Natural History</affiliation>
    </creator>
    <creator>
      <creatorName>Penev, Lyubomir</creatorName>
      <givenName>Lyubomir</givenName>
      <familyName>Penev</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-2186-5033</nameIdentifier>
      <affiliation>Pensoft Publishers</affiliation>
    </creator>
    <creator>
      <creatorName>Dimitrova, Mariya</creatorName>
      <givenName>Mariya</givenName>
      <familyName>Dimitrova</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-8083-6048</nameIdentifier>
      <affiliation>Pensoft Publishers</affiliation>
    </creator>
    <creator>
      <creatorName>Csorba, Gabor</creatorName>
      <givenName>Gabor</givenName>
      <familyName>Csorba</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-5720-4600</nameIdentifier>
      <affiliation>Hungarian Natural History Museum</affiliation>
    </creator>
    <creator>
      <creatorName>Groom, Quentin</creatorName>
      <givenName>Quentin</givenName>
      <familyName>Groom</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-0596-5376</nameIdentifier>
      <affiliation>Agentschap Plantentuin Meise</affiliation>
    </creator>
    <creator>
      <creatorName>Willoughby, Anna</creatorName>
      <givenName>Anna</givenName>
      <familyName>Willoughby</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-0504-0605</nameIdentifier>
      <affiliation>University of Georgia: Athens, GA, US</affiliation>
    </creator>
  </creators>
  <titles>
    <title>CETAF-DiSSCo/COVID19-TAF biodiversity-related knowledge hub working group: indexed biotic interactions and review summary</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <subjects>
    <subject>biodiversity</subject>
    <subject>species interactions</subject>
    <subject>virus-host</subject>
    <subject>bats</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2020-05-22</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/3839098</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsSupplementTo" resourceTypeGeneral="Software">https://github.com/globalbioticinteractions/elton</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.3838240</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/covid-19</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/zenodo</relatedIdentifier>
  </relatedIdentifiers>
  <version>0.2</version>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;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/).&lt;/p&gt;

&lt;p&gt;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).&amp;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.&lt;/p&gt;

&lt;p&gt;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.&lt;/p&gt;

&lt;p&gt;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.&lt;/p&gt;

&lt;p&gt;Funding:&lt;br&gt;
The creation of this archive was made possible in part by reporting software developed as part of the National Science Foundation award &amp;quot;Collaborative Research: Digitization TCN: Digitizing collections to trace parasite-host associations and predict the spread of vector-borne disease,&amp;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 .&lt;/p&gt;

&lt;p&gt;References:&lt;br&gt;
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.&lt;/p&gt;

&lt;p&gt;GloBI Data Review Report&lt;/p&gt;

&lt;p&gt;Datasets under review:&lt;br&gt;
&amp;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&lt;br&gt;
&amp;nbsp;- De Rojas M, Do&amp;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&lt;br&gt;
&amp;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&lt;br&gt;
&amp;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&lt;br&gt;
&amp;nbsp;- Olival, K. J., Hosseini, P. R., Zambrana-Torrelio, C., Ross, N., Bogich, T. L., &amp;amp; Daszak, P. (2017). Host and viral traits predict zoonotic spillover from mammals. Nature, 546(7660), 646&amp;ndash;650. doi:10.1038/nature22975 accessed via https://github.com/globalbioticinteractions/olival2017/archive/f61070a5339d0e6c6e76d7eb4e2102decb52317d.zip on 2020-05-21T17:02:48.553Z&lt;br&gt;
&amp;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&lt;br&gt;
&amp;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&lt;br&gt;
&amp;nbsp;- Eneida L. Hatcher, Sergey A. Zhdanov, Yiming Bao, Olga Blinkova, Eric P. Nawrocki, Yuri Ostapchuck, Alejandro A. Sch&amp;auml;ffer, J. Rodney Brister, Virus Variation Resource &amp;ndash; improved response to emergent viral outbreaks, Nucleic Acids Research, Volume 45, Issue D1, January 2017, Pages D482&amp;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&lt;br&gt;
&amp;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&lt;/p&gt;

&lt;p&gt;Generated on:&lt;br&gt;
2020-05-22&lt;/p&gt;

&lt;p&gt;by:&lt;br&gt;
GloBI&amp;#39;s Elton 0.9.8&lt;br&gt;
(see https://github.com/globalbioticinteractions/elton).&lt;/p&gt;

&lt;p&gt;Note that all files ending with .tsv are files formatted&lt;br&gt;
as UTF8 encoded tab-separated values files.&lt;/p&gt;

&lt;p&gt;https://www.iana.org/assignments/media-types/text/tab-separated-values&lt;/p&gt;

&lt;p&gt;&lt;br&gt;
Included in this review archive are:&lt;/p&gt;

&lt;p&gt;README:&lt;br&gt;
&amp;nbsp; This file (lightly edited after initial automated generation).&lt;/p&gt;

&lt;p&gt;review_summary.tsv:&lt;br&gt;
&amp;nbsp; Summary across all reviewed collections of total number of distinct review comments.&lt;/p&gt;

&lt;p&gt;review_summary_by_collection.tsv:&lt;br&gt;
&amp;nbsp; Summary by reviewed collection of total number of distinct review comments.&lt;/p&gt;

&lt;p&gt;indexed_interactions_by_collection.tsv:&lt;br&gt;
&amp;nbsp; Summary of number of indexed interaction records by institutionCode and collectionCode.&lt;/p&gt;

&lt;p&gt;review_comments.tsv.gz:&lt;br&gt;
&amp;nbsp; All review comments by collection.&lt;/p&gt;

&lt;p&gt;indexed_interactions_full.tsv.gz:&lt;br&gt;
&amp;nbsp; All indexed interactions for all reviewed collections.&lt;/p&gt;

&lt;p&gt;indexed_interactions_simple.tsv.gz:&lt;br&gt;
&amp;nbsp; All indexed interactions for all reviewed collections selecting only sourceInstitutionCode, sourceCollectionCode, sourceCatalogNumber, sourceTaxonName, interactionTypeName and targetTaxonName.&lt;/p&gt;

&lt;p&gt;datasets_under_review.tsv:&lt;br&gt;
&amp;nbsp; Details on the datasets under review.&lt;/p&gt;

&lt;p&gt;elton.jar:&lt;br&gt;
&amp;nbsp; Program used to update datasets and generate the review reports and associated indexed interactions.&lt;/p&gt;

&lt;p&gt;datasets.zip:&lt;br&gt;
&amp;nbsp; source datasets collected by elton in process of executing the generate_report.sh script.&lt;/p&gt;

&lt;p&gt;generate_report.sh:&lt;br&gt;
&amp;nbsp; program used to generate the report&lt;/p&gt;

&lt;p&gt;generate_report.log:&lt;br&gt;
&amp;nbsp; log file generated as part of running the generate_report.sh script&lt;/p&gt;</description>
  </descriptions>
</resource>
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