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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.8.134931</article-id>
      <article-id pub-id-type="publisher-id">134931</article-id>
      <article-id pub-id-type="manuscript">25522</article-id>
      <article-categories>
        <subj-group subj-group-type="heading">
          <subject>Conference Abstract</subject>
        </subj-group>
        <subj-group subj-group-type="conference-part">
          <subject>SYM13 - Controlled Vocabularies: The secret sauce that unlocks the power of data consistency and accessibility!</subject>
        </subj-group>
        <subj-group subj-group-type="biological_taxon">
          <subject>Animalia</subject>
          <subject>Archaea</subject>
          <subject>Bacteria</subject>
          <subject>Chromista</subject>
          <subject>Fungi</subject>
          <subject>Plantae</subject>
          <subject>Protozoa</subject>
        </subj-group>
        <subj-group subj-group-type="scientific_subject">
          <subject>Computer &amp; Information sciences</subject>
          <subject>Life sciences</subject>
          <subject>Mycology</subject>
          <subject>Natural History</subject>
          <subject>Palaeontology</subject>
          <subject>Plant and habitat conservation</subject>
          <subject>Systematics</subject>
          <subject>Zoology &amp; Animal Biology</subject>
        </subj-group>
        <subj-group subj-group-type="geographical_area">
          <subject>World</subject>
        </subj-group>
      </article-categories>
      <title-group>
        <article-title>Automatically Generated Texts for Fauna and Flora from Structured Data Based on a Controlled Vocabulary</article-title>
      </title-group>
      <contrib-group content-type="authors">
        <contrib contrib-type="author" corresp="yes">
          <name name-style="western">
            <surname>Kerner</surname>
            <given-names>Adeline</given-names>
          </name>
          <email xlink:type="simple">kerner@mnhn.fr</email>
          <uri content-type="orcid">https://orcid.org/0000-0002-0101-8662</uri>
          <xref ref-type="aff" rid="A1">1</xref>
        </contrib>
        <contrib contrib-type="author" corresp="no">
          <name name-style="western">
            <surname>Saliba</surname>
            <given-names>Elie M.</given-names>
          </name>
          <uri content-type="orcid">https://orcid.org/0000-0001-9591-5016</uri>
          <xref ref-type="aff" rid="A2">2</xref>
        </contrib>
        <contrib contrib-type="author" corresp="no">
          <name name-style="western">
            <surname>Bailly</surname>
            <given-names>Nicolas</given-names>
          </name>
          <uri content-type="orcid">https://orcid.org/0000-0003-4994-0653</uri>
          <xref ref-type="aff" rid="A3">3</xref>
        </contrib>
        <contrib contrib-type="author" corresp="no">
          <name name-style="western">
            <surname>Bourgoin</surname>
            <given-names>Thierry</given-names>
          </name>
          <uri content-type="orcid">https://orcid.org/0000-0001-9277-2478</uri>
          <xref ref-type="aff" rid="A2">2</xref>
        </contrib>
        <contrib contrib-type="author" corresp="no">
          <name name-style="western">
            <surname>Vignes Lebbe</surname>
            <given-names>Régine</given-names>
          </name>
          <uri content-type="orcid">https://orcid.org/0000-0002-6912-6248</uri>
          <xref ref-type="aff" rid="A2">2</xref>
        </contrib>
      </contrib-group>
      <aff id="A1">
        <label>1</label>
        <addr-line content-type="verbatim">UMR 7207 – Centre de Recherche en Paléontologie - Paris CNRS – Sorbonne Université - MNHN, Paris, France</addr-line>
        <institution>UMR 7207 – Centre de Recherche en Paléontologie - Paris CNRS – Sorbonne Université - MNHN</institution>
        <addr-line content-type="city">Paris</addr-line>
        <country>France</country>
      </aff>
      <aff id="A2">
        <label>2</label>
        <addr-line content-type="verbatim">Institut de Systématique, Evolution, Biodiversité (ISYEB), MNHN, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France</addr-line>
        <institution>Institut de Systématique, Evolution, Biodiversité (ISYEB), MNHN, CNRS, Sorbonne Université, EPHE, Université des Antilles</institution>
        <addr-line content-type="city">Paris</addr-line>
        <country>France</country>
      </aff>
      <aff id="A3">
        <label>3</label>
        <addr-line content-type="verbatim">University of British Columbia / Beaty Biodiversity Museum, Vancouver, Canada</addr-line>
        <institution>University of British Columbia / Beaty Biodiversity Museum</institution>
        <addr-line content-type="city">Vancouver</addr-line>
        <country>Canada</country>
      </aff>
      <author-notes>
        <fn fn-type="corresp">
          <p>Corresponding author: Adeline Kerner (<email xlink:type="simple">kerner@mnhn.fr</email>).</p>
        </fn>
        <fn fn-type="edited-by">
          <p>Academic editor: </p>
        </fn>
      </author-notes>
      <pub-date pub-type="collection">
        <year>2024</year>
      </pub-date>
      <pub-date pub-type="epub">
        <day>19</day>
        <month>08</month>
        <year>2024</year>
      </pub-date>
      <volume>8</volume>
      <elocation-id>e134931</elocation-id>
      <uri content-type="arpha" xlink:href="http://openbiodiv.net/F5E33CAA-70F5-5636-B1CF-B674C318CF8C">F5E33CAA-70F5-5636-B1CF-B674C318CF8C</uri>
      <permissions>
        <copyright-statement>Adeline Kerner, Elie M. Saliba, Nicolas Bailly, Thierry Bourgoin, Régine Vignes Lebbe</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>Information systems like <ext-link ext-link-type="uri" xlink:href="https://xper3.fr/en/the-biodiversity-collaborative-management-platform/">Xper3</ext-link> and Fulgoromorpha Lists On the Web (<ext-link ext-link-type="uri" xlink:href="https://flow.hemiptera-databases.org/">FLOW</ext-link>) play a crucial role in managing and using biological data. These platforms store extensive collections of normalized data and structured taxonomic descriptions. By using controlled terminologies, they standardize the vocabulary, significantly enhancing the processes of identification, description, and comparison of various taxa. The massive assemblages of data hosted in these repositories could be reused to generate texts in natural languages automatically. The most immediate goal is to produce, from these information systems, more accessible and user-friendly displays in the form of taxon summary pages. </p>
        <p>This automated production of textual outputs is a great addition that can be continuously updated as the databases evolve. Can structured data be reused to provide better species pages and to ensure updating if the data evolves? Will AI assist in this process, or will specific computing be needed? To address these questions, multiple possible approaches have been identified.</p>
        <p>The most basic level of this process involves converting a single line from a taxon-by-character matrix into text that resembles natural language, similar to the descriptions found in botanical or zoological guides. The primary goal is to move beyond the rigid format of matrix lines or lists of characteristics (such as characters and states) of a species, and instead generate a coherent, easy-to-read paragraph intended for human eyes.</p>
        <p>To achieve this objective, a first solution is given by <italic>Descrxp</italic>, a tool currently developed in conjunction with Xper. The user specifies the desired key outline for the output, and <italic>Descrxp</italic> fills this canvas using the database contents. While this approach is highly reliable and adaptable to various contexts, its drawback is being labor-intensive, and requiring significant human input and oversight (Fig. <xref ref-type="fig" rid="F11816364">1</xref>).</p>
        <p>The second solution uses AI. Data on well-known taxa, and on more obscure taxa have been tested with <ext-link ext-link-type="uri" xlink:href="https://openai.com/chatgpt/">ChatGPT 3.5 or 4.0</ext-link>. ChatGPT succeeds well at generating natural language descriptions for well-known taxa (Fig. <xref ref-type="fig" rid="F11816399">2</xref>), providing text that appears accurate and coherent due to the extensive information available online for these groups.</p>
        <p>However, when it comes to more obscure taxa, less represented on the internet, the results can be more inconsistent and unpredictable (Fig. <xref ref-type="fig" rid="F11814680">3</xref>). This variability can be explained by the quality of the data the model has been trained on, which is significantly richer for well-known species. Consequently, for lesser-known groups, the generated descriptions may lack the precision and reliability seen with more familiar taxa. </p>
        <p>However, if more careful attention is given to the output of chatGPT (Fig. <xref ref-type="fig" rid="F11814682">4</xref>), it is possible to notice that the AI filled part of the description with inaccurate characters. Due to its inability to recognize specific scientific terminology, and to process hierarchical information, chatGPT ends up producing an over-generalized and redundant description. </p>
        <p>To go further, it would be possible to use a comparison between taxa to produce a text that highlights the remarkable features of a taxon. Moreover, it could be interesting to try and synthesize several lines of the initial matrix to extract generalized descriptions of groups of taxa, such as the description of a genus based on its included species. </p>
        <p>Using data from FLOW, Fishbase, and Xper3, the French ACDC (Counterfactual Learning for Controlled Data-to-text) project is creating a variety of text outputs. These range from "fill-in-the-blank" canvas to fully AI-generated content, utilizing data matrices derived from these pilot databases.</p>
      </abstract>
      <kwd-group>
        <label>Keywords</label>
        <kwd>AI</kwd>
        <kwd>data-to-text</kwd>
        <kwd>Xper3</kwd>
      </kwd-group>
      <counts>
        <fig-count count="4"/>
        <table-count count="0"/>
        <ref-count count="1"/>
      </counts>
    </article-meta>
    <notes>
      <sec sec-type="Presenting author">
        <title>Presenting author</title>
        <p>Adeline Kerner</p>
      </sec>
      <sec sec-type="Presented at">
        <title>Presented at</title>
        <p>SPNHC-TDWG 2024</p>
      </sec>
      <sec sec-type="Funding program">
        <title>Funding program</title>
        <p>ACDC (Counterfactual Learning for Controlled Data-to-text) project, ANR-21-CE23-0007</p>
      </sec>
    </notes>
  </front>
  
  <back>
    <sec sec-type="Conflicts of interest">
      <title>Conflicts of interest</title>
      <p>No conflict of interest to declare</p>
      <p>Disclaimer: This article is (co-)authored by any of the Editors-in-Chief, Managing Editors or their deputies in this journal.</p>
    </sec>
    <ref-list>
      <title>References</title>
      <ref id="B11814667">
        <element-citation publication-type="article">
          <person-group person-group-type="author">
            <name name-style="western">
              <surname>Debrenne</surname>
              <given-names>F.</given-names>
            </name>
            <name name-style="western">
              <surname>Zhuravlev</surname>
              <given-names>A. Yu.</given-names>
            </name>
            <name name-style="western">
              <surname>Kruse</surname>
              <given-names>P. D.</given-names>
            </name>
          </person-group>
          <year>2012</year>
          <article-title>Treatise Online no. 50: Part E, Revised, Volume 4, Chapter 19: Systematic descriptions: Archaeocyatha</article-title>
          <source>Treatise Online</source>
          <pub-id pub-id-type="doi">10.17161/to.v0i0.4335</pub-id>
        </element-citation>
      </ref>
    </ref-list>
  </back>
  <floats-group>
    <fig id="F11816364" position="float" orientation="portrait">
      <object-id content-type="arpha">E172B520-DFC0-59DE-BE55-5D6F22B2D630</object-id>
      
      <label>Figure 1.</label>
      <caption>
        <p>On the left, a key outline defining how to describe the male genitalia (case of an Xper3 database on phlebotomine sandflies, Diptera). On the right, three text descriptions generated from this template, based on data from three different species.</p>
      </caption>
      <graphic xlink:href="biss-08-e134931-g001.png" position="float" id="oo_1090787.png" orientation="portrait" xlink:type="simple">
        <uri content-type="original_file">https://binary.pensoft.net/fig/1090787</uri>
      </graphic>
    </fig>
    <fig id="F11816399" position="float" orientation="portrait">
      <object-id content-type="arpha">54559A05-0021-508E-99C7-254698367491</object-id>
      
      <label>Figure 2.</label>
      <caption>
        <p>On data related to common species (e.g., in <italic>Pinus</italic>), ChatGPT produces satisfactory texts (input on the left, output on the right).</p>
      </caption>
      <graphic xlink:href="biss-08-e134931-g002.png" position="float" id="oo_1090794.png" orientation="portrait" xlink:type="simple">
        <uri content-type="original_file">https://binary.pensoft.net/fig/1090794</uri>
      </graphic>
    </fig>
    <fig id="F11814680" position="float" orientation="portrait">
      <object-id content-type="arpha">1C21FA0B-8511-5A0A-BC2A-58E5966C2A79</object-id>
      
      <label>Figure 3.</label>
      <caption>
        <p>Example with a database on Archaeocyatha (A) Genus sheet from Xper3 (B) Description generated by chatGPT 4.0 based on a knowledge base whose data are structured with several levels of dependencies (C) Description generated by chatGPT 4.0 based on a knowledge base whose data have a minimal hierarchical structure.</p>
      </caption>
      <graphic xlink:href="biss-08-e134931-g003.png" position="float" id="oo_1090420.png" orientation="portrait" xlink:type="simple">
        <uri content-type="original_file">https://binary.pensoft.net/fig/1090420</uri>
      </graphic>
    </fig>
    <fig id="F11814682" position="float" orientation="portrait">
      <object-id content-type="arpha">48607201-DED0-5D3A-B332-88360A8475BE</object-id>
      
      <label>Figure 4.</label>
      <caption>
        <p>On the left: same description generated with chatGPT 4.0 as Fig. <xref ref-type="fig" rid="F11814680">3</xref>C. On the right the description from the reference treatise (<xref ref-type="bibr" rid="B11814667">Debrenne et al. 2012</xref>). Equivalent structures are denoted by the same colors. The red part is a random add-on.</p>
      </caption>
      <graphic xlink:href="biss-08-e134931-g004.png" position="float" id="oo_1090426.png" orientation="portrait" xlink:type="simple">
        <uri content-type="original_file">https://binary.pensoft.net/fig/1090426</uri>
      </graphic>
    </fig>
  </floats-group>
</article>
