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  <front>
    <journal-meta>
      <journal-id journal-id-type="publisher-id">63</journal-id>
      <journal-id journal-id-type="index">urn:lsid:arphahub.com:pub:0E0032F4-55AE-5263-8B3C-F4DD637C30C2</journal-id>
      <journal-title-group>
        <journal-title xml:lang="en">Biodiversity Information Science and Standards</journal-title>
        <abbrev-journal-title xml:lang="en">BISS</abbrev-journal-title>
      </journal-title-group>
      <issn pub-type="epub">2535-0897</issn>
      <publisher>
        <publisher-name>Pensoft Publishers</publisher-name>
      </publisher>
    </journal-meta>
    <article-meta>
      <article-id pub-id-type="doi">10.3897/biss.6.93707</article-id>
      <article-id pub-id-type="publisher-id">93707</article-id>
      <article-id pub-id-type="manuscript">20318</article-id>
      <article-categories>
        <subj-group subj-group-type="heading">
          <subject>Conference Abstract</subject>
        </subj-group>
        <subj-group subj-group-type="conference-part">
          <subject>SYM04 - Sharing and visualizing species data and information</subject>
        </subj-group>
      </article-categories>
      <title-group>
        <article-title>Synospecies, a Linked Data Application to Explore Taxonomic Names</article-title>
      </title-group>
      <contrib-group content-type="authors">
        <contrib contrib-type="author" corresp="no">
          <name name-style="western">
            <surname>Gmür</surname>
            <given-names>Reto</given-names>
          </name>
          <xref ref-type="aff" rid="A1">1</xref>
        </contrib>
        <contrib contrib-type="author" corresp="yes">
          <name name-style="western">
            <surname>Agosti</surname>
            <given-names>Donat</given-names>
          </name>
          <email xlink:type="simple">agosti@plazi.org</email>
          <uri content-type="orcid">https://orcid.org/0000-0001-9286-1200</uri>
          <xref ref-type="aff" rid="A1">1</xref>
        </contrib>
        <contrib contrib-type="author" corresp="no">
          <name name-style="western">
            <surname>Sautter</surname>
            <given-names>Guido</given-names>
          </name>
          <xref ref-type="aff" rid="A1">1</xref>
        </contrib>
      </contrib-group>
      <aff id="A1">
        <label>1</label>
        <addr-line content-type="verbatim">Plazi, Bern, Switzerland</addr-line>
        <institution>Plazi</institution>
        <addr-line content-type="city">Bern</addr-line>
        <country>Switzerland</country>
      </aff>
      <author-notes>
        <fn fn-type="corresp">
          <p>Corresponding author: Donat Agosti (<email xlink:type="simple">agosti@plazi.org</email>).</p>
        </fn>
        <fn fn-type="edited-by">
          <p>Academic editor: </p>
        </fn>
      </author-notes>
      <pub-date pub-type="collection">
        <year>2022</year>
      </pub-date>
      <pub-date pub-type="epub">
        <day>23</day>
        <month>08</month>
        <year>2022</year>
      </pub-date>
      <volume>6</volume>
      <elocation-id>e93707</elocation-id>
      <uri content-type="arpha" xlink:href="http://openbiodiv.net/201DB444-8827-5128-B06F-72181542ED09">201DB444-8827-5128-B06F-72181542ED09</uri>
      <permissions>
        <copyright-statement>Reto Gmür, Donat Agosti, Guido Sautter</copyright-statement>
        <license license-type="creative-commons-attribution" xlink:href="http://creativecommons.org/licenses/by/4.0/" xlink:type="simple">
          <license-p>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.</license-p>
        </license>
      </permissions>
      <abstract>
        <label>Abstract</label>
        <p>Synospecies is a linked data application to explore changes in taxonomic names (<xref ref-type="bibr" rid="B7974872">Gmür and Agosti 2021</xref>). The underlying source of truth for the establishment of taxa, the assignment and re-assignment of names, are taxonomic treatments. Taxonomic treatments are sections of publications documenting the features or distribution of taxa in ways adhering to highly formalized conventions, and published in scientific journals, which shape our understanding of global biodiversity (<xref ref-type="bibr" rid="B7974901">Catapano 2010</xref>). Plazi, a not-for-profit organization dedicated to liberating knowledge, extracts the relevant information from these treatments and makes it publicly available in digital form. Depending on the original form of a publication, a treatment undergoes several steps during its processing. All these steps affect the available digital artifacts extracted from the treatment's original publication. The treatments are digitalized, the text is annotated with a specialized editor, and cross-referenced and enhanced with other sources (<xref ref-type="bibr" rid="B7974910">Agosti and Sautter 2018</xref>). After these steps, the annotated text is transformed to the different structured data-formats used by other digital biodiversity platforms (e.g., Global Biodiversity Information Facility: <ext-link ext-link-type="uri" xlink:href="https://www.gbif.org/publisher/7ce8aef0-9e92-11dc-8738-b8a03c50a862">Plazi.org taxonomic treatment database</ext-link> using Darwin Core Archive, generic linked data tools (e.g. <ext-link ext-link-type="uri" xlink:href="https://www.lodview.it/lodview/?IRI=http%3A%2F%2Ftreatment.plazi.org%2Fid%2F03ACBF18FFDF1B3AFF31FA64FC1AEA83&amp;sparql=%3C%3E&amp;prefix=http%3A%2F%2Ftreatment.plazi.org%2F">lod view</ext-link>; <ext-link ext-link-type="uri" xlink:href="http://rdf2h-browser.linked.solutions/#http://treatment.plazi.org/id/03ACBF18FFDF1B3AFF31FA64FC1AEA83">RDF2h Browser</ext-link>) and other consuming applications (e.g <ext-link ext-link-type="uri" xlink:href="https://ocellus.info/">Ocellus</ext-link> via <ext-link ext-link-type="uri" xlink:href="https://zenodeo.org/about">Zenodeo</ext-link> using XML; <ext-link ext-link-type="uri" xlink:href="https://openbiodiv.net/">openBioDiv </ext-link>using XML; <ext-link ext-link-type="uri" xlink:href="https://github.com/jhpoelen/hmw">HMW</ext-link> using XML; <ext-link ext-link-type="uri" xlink:href="http://denver.hesge.ch/biotic/demo/">Biotic interaction browser</ext-link> using TaxPub XML; <ext-link ext-link-type="uri" xlink:href="https://opendata.swiss/de/dataset/plazi-treatmentbank">opendata.swiss</ext-link> using RDF)  .</p>
        <p>While these transformations have been taking place for a long time now, Plazi is now experimenting with making this process more transparent: with the Plazi Actionable Accessible Archive (PAAA) architecture both addition and modification of the digitalized treatments trigger an extensible set of workflows that are immediately executed on the GitHub platform. Not only is the exact definition and code of every workflow publicly accessible, but the results, errors and execution time of every single workflow is accessible as well. This offers an unprecedented degree of transparency and flexibility in the data processing that we have prototypically implemented for the creation of the RDF data used by Synospecies. As with the W3C GRDDL recommendation (<ext-link ext-link-type="uri" xlink:href="https://www.w3.org/TR/grddl/">https://www.w3.org/TR/grddl/</ext-link>) XSLT is used to transform XML to RDF/XML, a concrete syntax of the early days of RDF still supported by most RDF tools, allowing the data to be read as RDF. The used XSLT document is part of the bundled gg2rdf GitHub action (<ext-link ext-link-type="uri" xlink:href="http://github.com/plazi/gg2rdf">https://github.com/plazi/gg2rdf</ext-link>) together with the other transformation steps required to generate a transformation result in the both human- and machine-readable RDF Turtle format. On the GitHub Actions page of the treatments-xml repository (<ext-link ext-link-type="uri" xlink:href="http://github.com/plazi/treatments-xml/actions">https://github.com/plazi/treatments-xml/actions</ext-link>) one can see that every commit to this repository triggers a workflow run that takes approximately 12 minutes to execute. After that the transformation results are available in the treatments-rdf repository (<ext-link ext-link-type="uri" xlink:href="http://github.com/plazi/treatments-rdf/">https://github.com/plazi/treatments-rdf/</ext-link>). The commit of RDF data to the treatments-rdf repository triggers a webhook that loads the newly added data to the Plazi triplestore making it virtually immediately available in Synospecies.</p>
      </abstract>
      <kwd-group>
        <label>Keywords</label>
        <kwd>biodiversity</kwd>
        <kwd>RDF</kwd>
        <kwd>knowledge graph</kwd>
        <kwd>treatment</kwd>
        <kwd>citation</kwd>
        <kwd>ontology</kwd>
        <kwd>SPARQL</kwd>
        <kwd>TreatmentBank</kwd>
      </kwd-group>
      <counts>
        <fig-count count="0"/>
        <table-count count="0"/>
        <ref-count count="3"/>
      </counts>
    </article-meta>
    <notes>
      <sec sec-type="Presenting author">
        <title>Presenting author</title>
        <p>Reto Gmür</p>
      </sec>
      <sec sec-type="Presented at">
        <title>Presented at</title>
        <p>TDWG 2022 </p>
      </sec>
      <sec sec-type="Funding program">
        <title>Funding program</title>
        <p>The TreatmentBank infrastructure is supported by the Horizon Europe funded project <ext-link ext-link-type="uri" xlink:href="https://bicikl-project.eu/">Biodiversity Community Integrated Knowledge Library </ext-link> (BiCIKL), the <ext-link ext-link-type="uri" xlink:href="https://www.arcadiafund.org.uk/">Arcadia Fund</ext-link> and the <ext-link ext-link-type="uri" xlink:href="https://www.swissuniversities.ch/themen/digitalisierung/open-science-2021-2024">Swissuniversities</ext-link> funded <ext-link ext-link-type="uri" xlink:href="https://ebiodiv.org/">eBioDiv</ext-link> project. </p>
        <p>BiCIKL <ext-link ext-link-type="uri" xlink:href="https://bicikl-project.eu/">https://bicikl-project.eu/</ext-link>  grant number 101007492</p>
        <p>Arcadia Fund <ext-link ext-link-type="uri" xlink:href="https://www.arcadiafund.org.uk/">https://www.arcadiafund.org.uk/</ext-link></p>
        <p>Swissuniversities <ext-link ext-link-type="uri" xlink:href="https://www.swissuniversities.ch/themen/digitalisierung/open-science-2021-2024">https://www.swissuniversities.ch/themen/digitalisierung/open-science-2021-2024</ext-link></p>
        <p>eBioDiv <ext-link ext-link-type="uri" xlink:href="https://urldefense.com/v3/__https://ebiodiv.org/__;!!DZ3fjg!_awKzBhd7sx9MvrCPNHdCsNP9VS8DhZiNb4KVjqRY0asDWxuEGnPkpHmzW4qnwJL23aa_mVUykGSUTxV$">https://ebiodiv.org/</ext-link></p>
      </sec>
    </notes>
  </front>
  
  <back>
    <sec sec-type="Funding program">
      <title>Funding program</title>
      <p>The TreatmentBank infrastructure is supported by the Horizon Europe funded project <ext-link ext-link-type="uri" xlink:href="https://bicikl-project.eu/">Biodiversity Community Integrated Knowledge Library </ext-link> (BiCIKL), the <ext-link ext-link-type="uri" xlink:href="https://www.arcadiafund.org.uk/">Arcadia Fund</ext-link> and the <ext-link ext-link-type="uri" xlink:href="https://www.swissuniversities.ch/themen/digitalisierung/open-science-2021-2024">Swissuniversities</ext-link> funded <ext-link ext-link-type="uri" xlink:href="https://ebiodiv.org/">eBioDiv</ext-link> project. </p>
      <p>BiCIKL <ext-link ext-link-type="uri" xlink:href="https://bicikl-project.eu/">https://bicikl-project.eu/</ext-link>  grant number 101007492</p>
      <p>Arcadia Fund <ext-link ext-link-type="uri" xlink:href="https://www.arcadiafund.org.uk/">https://www.arcadiafund.org.uk/</ext-link></p>
      <p>Swissuniversities <ext-link ext-link-type="uri" xlink:href="https://www.swissuniversities.ch/themen/digitalisierung/open-science-2021-2024">https://www.swissuniversities.ch/themen/digitalisierung/open-science-2021-2024</ext-link></p>
      <p>eBioDiv <ext-link ext-link-type="uri" xlink:href="https://urldefense.com/v3/__https://ebiodiv.org/__;!!DZ3fjg!_awKzBhd7sx9MvrCPNHdCsNP9VS8DhZiNb4KVjqRY0asDWxuEGnPkpHmzW4qnwJL23aa_mVUykGSUTxV$">https://ebiodiv.org/</ext-link></p>
    </sec>
    <ref-list>
      <title>References</title>
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            <name name-style="western">
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            </name>
            <name name-style="western">
              <surname>Sautter</surname>
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            </name>
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        </element-citation>
      </ref>
      <ref id="B7974901">
        <element-citation publication-type="article">
          <person-group person-group-type="author">
            <name name-style="western">
              <surname>Catapano</surname>
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            </name>
          </person-group>
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          <person-group person-group-type="author">
            <name name-style="western">
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              <surname>Agosti</surname>
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        </element-citation>
      </ref>
    </ref-list>
  </back>
</article>
