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  <front>
    <journal-meta>
      <journal-id journal-id-type="publisher-id">17</journal-id>
      <journal-id journal-id-type="index">urn:lsid:arphahub.com:pub:8E638694-B4E0-570A-856A-746FF325BF6B</journal-id>
      <journal-title-group>
        <journal-title xml:lang="en">Research Ideas and Outcomes</journal-title>
        <abbrev-journal-title xml:lang="en">RIO</abbrev-journal-title>
      </journal-title-group>
      <issn pub-type="epub">2367-7163</issn>
      <publisher>
        <publisher-name>Pensoft Publishers</publisher-name>
      </publisher>
    </journal-meta>
    <article-meta>
      <article-id pub-id-type="doi">10.3897/rio.8.e95770</article-id>
      <article-id pub-id-type="publisher-id">95770</article-id>
      <article-id pub-id-type="manuscript">20555</article-id>
      <article-categories>
        <subj-group subj-group-type="heading">
          <subject>Conference Abstract</subject>
        </subj-group>
        <subj-group subj-group-type="sdg">
          <subject>Industry</subject>
          <subject> innovation &amp; infrastructure</subject>
        </subj-group>
      </article-categories>
      <title-group>
        <article-title>A portal for indexing distributed FAIR digital objects for catalysis research</article-title>
      </title-group>
      <contrib-group content-type="authors">
        <contrib contrib-type="author" corresp="yes">
          <name name-style="western">
            <surname>Nieva de la Hidalga</surname>
            <given-names>Abraham</given-names>
          </name>
          <email xlink:type="simple">nievadelahidalgaa@cardiff.ac.uk</email>
          <uri content-type="orcid">https://orcid.org/0000-0001-7348-7612</uri>
          <xref ref-type="aff" rid="A1">1</xref>
          <xref ref-type="aff" rid="A2">2</xref>
        </contrib>
        <contrib contrib-type="author" corresp="no">
          <name name-style="western">
            <surname>Goodall</surname>
            <given-names>Josephine</given-names>
          </name>
          <xref ref-type="aff" rid="A1">1</xref>
          <xref ref-type="aff" rid="A2">2</xref>
        </contrib>
        <contrib contrib-type="author" corresp="no">
          <name name-style="western">
            <surname>Catlow</surname>
            <given-names>Richard A.</given-names>
          </name>
          <xref ref-type="aff" rid="A3">3</xref>
          <xref ref-type="aff" rid="A1">1</xref>
          <xref ref-type="aff" rid="A2">2</xref>
        </contrib>
        <contrib contrib-type="author" corresp="no">
          <name name-style="western">
            <surname>Anyka</surname>
            <given-names>Corinne</given-names>
          </name>
          <xref ref-type="aff" rid="A4">4</xref>
          <xref ref-type="aff" rid="A2">2</xref>
          <xref ref-type="aff" rid="A5">5</xref>
        </contrib>
        <contrib contrib-type="author" corresp="no">
          <name name-style="western">
            <surname>Matthews</surname>
            <given-names>Brian</given-names>
          </name>
          <xref ref-type="aff" rid="A6">6</xref>
        </contrib>
      </contrib-group>
      <aff id="A1">
        <label>1</label>
        <addr-line content-type="verbatim">School of Chemistry Cardiff University, Cardiff, United Kingdom</addr-line>
        <institution>School of Chemistry Cardiff University</institution>
        <addr-line content-type="city">Cardiff</addr-line>
        <country>United Kingdom</country>
      </aff>
      <aff id="A2">
        <label>2</label>
        <addr-line content-type="verbatim">UK Catalysis Hub, Harwell, United Kingdom</addr-line>
        <institution>UK Catalysis Hub</institution>
        <addr-line content-type="city">Harwell</addr-line>
        <country>United Kingdom</country>
      </aff>
      <aff id="A3">
        <label>3</label>
        <addr-line content-type="verbatim">University College London, London, United Kingdom</addr-line>
        <institution>University College London</institution>
        <addr-line content-type="city">London</addr-line>
        <country>United Kingdom</country>
      </aff>
      <aff id="A4">
        <label>4</label>
        <addr-line content-type="verbatim">School of Chemistry Cardiff University, Caridff, United Kingdom</addr-line>
        <institution>School of Chemistry Cardiff University</institution>
        <addr-line content-type="city">Caridff</addr-line>
        <country>United Kingdom</country>
      </aff>
      <aff id="A5">
        <label>5</label>
        <addr-line content-type="verbatim">Finden Ltd., Harwell, United Kingdom</addr-line>
        <institution>Finden Ltd.</institution>
        <addr-line content-type="city">Harwell</addr-line>
        <country>United Kingdom</country>
      </aff>
      <aff id="A6">
        <label>6</label>
        <addr-line content-type="verbatim">Scientific Computing Department, Science and Technology Facilities Council, Harwell, United Kingdom</addr-line>
        <institution>Scientific Computing Department, Science and Technology Facilities Council</institution>
        <addr-line content-type="city">Harwell</addr-line>
        <country>United Kingdom</country>
      </aff>
      <author-notes>
        <fn fn-type="corresp">
          <p>Corresponding author: Abraham Nieva de la Hidalga (<email xlink:type="simple">nievadelahidalgaa@cardiff.ac.uk</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>12</day>
        <month>10</month>
        <year>2022</year>
      </pub-date>
      <volume>8</volume>
      <elocation-id>e95770</elocation-id>
      <uri content-type="arpha" xlink:href="http://openbiodiv.net/8A3540BB-C826-59B5-B750-2D173ED0A435">8A3540BB-C826-59B5-B750-2D173ED0A435</uri>
      <permissions>
        <copyright-statement>Abraham Nieva de la Hidalga, Josephine Goodall, Richard A. Catlow, Corinne Anyka, Brian Matthews</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>A research object (RO) is defined as a semantically rich aggregation of (potentially distributed) resources that provide a layer of structure on top of information delivered as linked data (<xref ref-type="bibr" rid="B8017946">Bechhofer et al. 2013</xref>, <xref ref-type="bibr" rid="B8017967">Soiland-Reyes et al. 2022</xref>). A RO provides a container for the aggregation of resources, produced, and consumed by common services and shareable within and across organisational boundaries. This work sees research digital objects as composites which may consist of objects hosted in different repositories.</p>
        <p>In catalysis research, the characterisation of a sample may require analysing experimental data obtained from an instrument, data from a computer model, and/or comparing to data from a specialized database. Additionally, data may need to be reduced and cleaned before analysis, resulting in intermediate data. In this scenario the composite research object is integrated by all these data objects and their corresponding metadata. <ext-link ext-link-type="uri" xlink:href="http://ukcatalysishub.co.uk">UK Catalysis Hub</ext-link><ext-link ext-link-type="uri" xlink:href="http://ukcatalysishub.co.uk"/> (UKCH) researchers perform these tasks as part of their day-to-day work. However, most of the time they need to manually collect, catalogue, and preserve all these data assets.</p>
        <p>The UKCH aims to support researchers with tools and services for the management and processing of data, through the development of the <ext-link ext-link-type="uri" xlink:href="http://cdi.ukcatalysishub.org/">Catalysis Data Infrastructure </ext-link>(CDI <xref ref-type="bibr" rid="B8018001">Nieva de la Hidalga et al. 2022a</xref>) and the <ext-link ext-link-type="uri" xlink:href="https://github.com/UK-Catalysis-Hub/XAS-Workflow-Demo">Catalysis Research Workbench</ext-link> (CRW <xref ref-type="bibr" rid="B8017988">Nieva de la Hidalga et al. 2022b</xref>). This work is integrated in the context of the <ext-link ext-link-type="uri" xlink:href="https://www.psdi.ac.uk/">Physical Sciences Data Infrastructure</ext-link><ext-link ext-link-type="uri" xlink:href="https://www.psdi.ac.uk/"> </ext-link>(PSDI <xref ref-type="bibr" rid="B8179161">Coles and Knight 2022</xref>). The PSDI aims to provide a layer that enables transparent access to existing resources whilst ensuring that they remain dedicated to its specific application. The intention is to explore the concept of the composite research digital object and the services required to facilitate both human and programmatic interactions with those objects to browse, review, retrieve, and use digital objects in the context of the research produced by UKCH scientists. The CDI will act as a thematic portal presenting data managed through the PSDI and serve as an example for the development of similar portals targeting specific research domains.</p>
        <p>In this case, the <ext-link ext-link-type="uri" xlink:href="http://cdi.ukcatalysishub.org/">CDI </ext-link>is in the process of being redesigned with a sematic metadata model. The basic ontologies being considered for this model are: DCAT (<xref ref-type="bibr" rid="B8018020">Albertoni et al. 2022</xref>) will encode the metadata of digital objects; PROV-O (<xref ref-type="bibr" rid="B8018033">Belhajjame et al. 2013</xref>) will track the generation of digital objects. SPAR (<xref ref-type="bibr" rid="B8018046">Peroni and Shotton 2018</xref>) to encode publications data; SCHOLIX to encode the links between publications and data objects (<xref ref-type="bibr" rid="B8018055">Burton et al. 2017</xref>); FOAF (<xref ref-type="bibr" rid="B8018090">Brickley and Miller 2014</xref>) to encode researcher information; the Organization Ontology (ORG <xref ref-type="bibr" rid="B8018148">Reynolds 2014</xref>) to encode institution information; EXPO (<xref ref-type="bibr" rid="B8018189">Soldatova et al. 2006</xref>) to encode experiment information; and various domain specific ontologies for adding metadata about experiments, for instance CHEBI (<xref ref-type="bibr" rid="B8018122">Hastings et al. 2011</xref>), CHEMINF (<xref ref-type="bibr" rid="B8018133">Hastings et al. 2015</xref>), and FIX (<xref ref-type="bibr" rid="B8018112">Chebi-Administrators 2005</xref>).</p>
        <p>The implementation of the CDI using these ontologies will provide a roadmap for the integration of FAIR data object repositories with a service infrastructure which supports reproducibility, reuse of data, reuse of processing tools and implementation of advanced processing tools.</p>
        <p>The integration of the CDI and CRW with existing and new infrastructures will further support the work of catalysis scientists. In this context, a researcher can access the CDI to look for publications, see if there are data objects linked to them, and then look for processing tools which can be used to reproduce the results. An experiment for an early use case demonstrated the feasibility of reproducing published results using data and metadata linked to existing publications (<xref ref-type="bibr" rid="B8017988">Nieva de la Hidalga et al. 2022b</xref>). In the experiment, papers citing processable data were used to retrieve, process, and reproduce published results with no need for contacting the authors. Fig. <xref ref-type="fig" rid="F8018259">1</xref> presents a view of the experiment performed.</p>
        <p>The current practices of publishing catalysis research data can be seen as aligned to the FAIR data principles, for instance Fig. <xref ref-type="fig" rid="F8018259">1</xref> above can be also seen as Fig. <xref ref-type="fig" rid="F8018296">2</xref></p>
        <p>Reproducing results required several human-centered activities,  partly due to the encoding of the metadata as text documents. The challenge is to accelerate and automate these processes. It is important to highlight the role of cataloguing interfaces, such as the CDI, containing DO crates with only metadata and links to the different data assests that constitute the composite digital objects. The users of these interfaces will in turn rely on transparent services which do not require them to manually track the location and formats of the data assets they want to retrieve and use.</p>
      </abstract>
      <kwd-group>
        <label>Keywords</label>
        <kwd>Research data management</kwd>
        <kwd>Catalysis research data</kwd>
        <kwd>FAIR data principles</kwd>
        <kwd>Composite research object</kwd>
      </kwd-group>
      <counts>
        <fig-count count="2"/>
        <table-count count="0"/>
        <ref-count count="15"/>
      </counts>
    </article-meta>
    <notes>
      <sec sec-type="Presenting author">
        <title>Presenting author</title>
        <p>Abraham Nieva de la Hidalga</p>
      </sec>
      <sec sec-type="Presented at">
        <title>Presented at</title>
        <p>First International Conference on FAIR Digital Objects, presentation</p>
      </sec>
      <sec sec-type="Funding program">
        <title>Funding program</title>
        <p>UK Catalysis Hub is kindly thanked for resources and support provided via our membership of the UK Catalysis Hub Consortium and funded by EPSRC grant:  EP/R026939/1, EP/R026815/1, EP/R026645/1, EP/R027129/1 or EP/M013219/1(biocatalysis))</p>
      </sec>
      <sec sec-type="Hosting institution">
        <title>Hosting institution</title>
        <p>UK Catalysis Hub Research Complex at Harwell Rutherford Appleton Laboratory, R92 Harwell Oxford Oxfordshire OX11 0FA</p>
      </sec>
    </notes>
  </front>
  
  <back>
    <sec sec-type="Funding program">
      <title>Funding program</title>
      <p>UK Catalysis Hub is kindly thanked for resources and support provided via our membership of the UK Catalysis Hub Consortium and funded by EPSRC grant:  EP/R026939/1, EP/R026815/1, EP/R026645/1, EP/R027129/1 or EP/M013219/1(biocatalysis))</p>
    </sec>
    <sec sec-type="Hosting institution">
      <title>Hosting institution</title>
      <p>UK Catalysis Hub Research Complex at Harwell Rutherford Appleton Laboratory, R92 Harwell Oxford Oxfordshire OX11 0FA</p>
    </sec>
    <sec sec-type="Author contributions">
      <title>Author contributions</title>
      <p>ANH edited the abstract, JG and CA were responsible of curating the publications metadata, RC and BM reviewed the content and motivated the research project. All authors reviewed the contents of the abstract and agreed to its submission.</p>
    </sec>
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      <label>Figure 1.</label>
      <caption>
        <p>Reproduction Experiment. 1 Find Linked Data Objects. 2. Track data provenance (verify where published data comes from). 3 Map published data to results. 4 Reproduce Results (learn how results were obtained). 5 Automate Reproduction and Use alternative software.</p>
      </caption>
      <graphic xlink:href="rio-08-e95770-g001.png" position="float" id="oo_713690.png" orientation="portrait" xlink:type="simple">
        <uri content-type="original_file">https://binary.pensoft.net/fig/713690</uri>
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      <label>Figure 2.</label>
      <caption>
        <p>Alignment of published catalysis research data to the FAIR data principles.</p>
      </caption>
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        <uri content-type="original_file">https://binary.pensoft.net/fig/713691</uri>
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</article>
