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‎joss.00023/10.21105.joss.00023.crossref.xml

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<doi_batch version="4.3.7" xmlns="http://www.crossref.org/schema/4.3.7" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.crossref.org/schema/4.3.7 http://www.crossref.org/schemas/crossref4.3.7.xsd">
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<timestamp>20160531211646</timestamp>
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<depositor>
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<depositor_name>JOSS Admin</depositor_name>
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<email_address>[email protected]</email_address>
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</depositor>
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<registrant>The Open Journal</registrant>
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</head>
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<body>
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<journal>
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<journal_metadata>
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<full_title>The Journal of Open Source Software</full_title>
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<abbrev_title>JOSS</abbrev_title>
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<doi_data>
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<doi>10.21105/joss</doi>
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<resource>http://joss.theoj.org</resource>
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</doi_data>
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</journal_metadata>
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<journal_article publication_type="full_text">
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<titles>
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<title>Scowl: a Scala DSL for programming with the OWL API</title>
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</titles>
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<contributors><person_name sequence="first" contributor_role="author"><given_name>James</given_name><surname>P Balhoff</surname><ORCID>http://orcid.org/0000-0002-8688-6599</ORCID></person_name></contributors>
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<publication_date>
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<month>05</month>
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<day>31</day>
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<year>2016</year>
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<item_number>10.21105/joss.00023</item_number>
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<doi>10.21105/joss.00023</doi>
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<timestamp>20160531211646</timestamp>
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<resource>http://joss.theoj.org/papers/10.21105/joss.00023</resource>
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<citation_list><citation key="ref1"><unstructured_citation>The OWL API, http://owlapi.sourceforge.net/, \urlhttp://owlapi.sourceforge.net/</unstructured_citation></citation><citation key="ref2"><unstructured_citation>OWL 2 web ontology language manchester syntax, Horridge, Matthew and Patel-Schneider, Peter F, 2009, https://www.w3.org/TR/owl2-manchester-syntax/, \urlhttps://www.w3.org/TR/owl2-manchester-syntax/</unstructured_citation></citation><citation key="ref3"><unstructured_citation>OWL 2 web ontology language: Structural specification and functional-style syntax, Motik, Boris and Patel-Schneider, Peter F and Parsia, Bijan and Bock, Conrad and Fokoue, Achille and Haase, Peter and Hoekstra, Rinke and Horrocks, Ian and Ruttenberg, Alan and Sattler, Uli, 2009, https://www.w3.org/TR/owl2-syntax/, \urlhttps://www.w3.org/TR/owl2-syntax/</unstructured_citation></citation><citation key="ref4"><unstructured_citation>OWL 2 Web Ontology Language Document Overview, W3C OWL Working Group, 2009, https://www.w3.org/TR/owl2-overview/, \urlhttps://www.w3.org/TR/owl2-overview/</unstructured_citation></citation><citation key="ref5"><doi>10.1038/nbt1346</doi></citation></citation_list>
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‎joss.00023/10.21105.joss.00023.html

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body = <<-EOF
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<meta name="citation_title" content="Scowl: a Scala DSL for programming with the OWL API">
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<meta name="citation_author" content="P Balhoff, James">
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<meta name="citation_publication_date" content="2016/05/31">
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<meta name="citation_journal_title" content="The Journal of Open Source Software">
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<meta name="citation_pdf_url" content="https://github.com/openjournals/joss-papers/blob/master/joss.00023/10.21105.joss.00023.pdf">
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<div class="accepted-paper">
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<h1>Scowl: a Scala DSL for programming with the OWL API</h1>
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<div class="columns links">
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<div class="column four-fifths" style="padding-bottom: 10px;">
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<strong>Authors</strong>
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<ul class="author-list">
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<li><a href="http://orcid.org/0000-0002-8688-6599" target="_blank">James P Balhoff</a></li>
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</ul>
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</div>
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<div class="one-third column">
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<span class="repo">Repository:<br /><a href="https://github.com/phenoscape/scowl">Repository link &raquo;</a></span>
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</div>
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<div class="one-third column">
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<span class="paper">Paper:<br /><a href="https://github.com/openjournals/joss-papers/blob/master/joss.00023/10.21105.joss.00023.pdf">PDF link &raquo;</a></span>
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</div>
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<div class="one-third column">
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<span class="paper">Review:<br /><a href="https://github.com/openjournals/joss-reviews/issues/23">View review issue &raquo;</a></span>
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</div>
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<div class="one-third column" style="padding-top: 20px;">
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<span class="repo">DOI:<br /><a href="http://dx.doi.org/10.21105/joss.00023">http://dx.doi.org/10.21105/joss.00023</a></span>
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</div>
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<div class="one-third column" style="padding-top: 20px;">
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<span class="paper">Status badge:<br /><img src="http://joss.theoj.org/papers/10.21105/joss.00023/status.svg"></span>
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</div>
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<div class="one-third column" style="padding-top: 20px;">
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</div>
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</div>
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<div class="paper-body">
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<h1 id="summary">Summary</h1>
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<p>Scowl is a domain-specific language (DSL) which provides a convenient Scala-based syntax for composing OWL (Web Ontology Language, <span class="citation">(W3C OWL Working Group 2009)</span>) expressions and axioms. Effective use of complex, community developed ontologies within research applications, such as those from the OBO library (Open Biomedical Ontologies, <span class="citation">(Smith et al. 2007)</span>), often requires custom programmatic manipulation of ontologies and data, along with input to and output from automated reasoners. Allowing deeply nested OWL constructs to be coded in a readable, declarative style, Scowl facilitates use cases at the interface of application programming and OWL modeling: 1) tabular data ingest and transformation into OWL; 2) ontology manipulation via programmatic generation of axioms from existing content; and 3) reporting on ontology content using pattern matching on OWL objects.</p>
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<p>Within Scala applications, Scowl adds extension methods to native Java OWL API objects <span class="citation">(&#8220;The OWL API,&#8221; n.d.)</span>, supporting two syntax styles: the pseudo-English Manchester syntax <span class="citation">(Horridge and Patel-Schneider 2009)</span>, as well as the OWL Functional syntax <span class="citation">(Motik et al. 2009)</span>. Integration with the standard Java OWL API provides compatibility with multiple freely available OWL reasoners.</p>
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<h1 id="references" class="unnumbered">References</h1>
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<div id="refs" class="references">
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<div id="ref-Horridge2009">
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<p>Horridge, Matthew, and Peter F Patel-Schneider. 2009. &#8220;OWL 2 Web Ontology Language Manchester Syntax.&#8221; <a href="https://www.w3.org/TR/owl2-manchester-syntax/" class="uri">https://www.w3.org/TR/owl2-manchester-syntax/</a>. <a href="https://www.w3.org/TR/owl2-manchester-syntax/" class="uri">https://www.w3.org/TR/owl2-manchester-syntax/</a>.</p>
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</div>
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<div id="ref-Motik2009">
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<p>Motik, Boris, Peter F Patel-Schneider, Bijan Parsia, Conrad Bock, Achille Fokoue, Peter Haase, Rinke Hoekstra, Ian Horrocks, Alan Ruttenberg, and Uli Sattler. 2009. &#8220;OWL 2 Web Ontology Language: Structural Specification and Functional-Style Syntax.&#8221; <a href="https://www.w3.org/TR/owl2-syntax/" class="uri">https://www.w3.org/TR/owl2-syntax/</a>. <a href="https://www.w3.org/TR/owl2-syntax/" class="uri">https://www.w3.org/TR/owl2-syntax/</a>.</p>
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</div>
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<div id="ref-Smith2007">
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<p>Smith, Barry, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J Goldberg, et al. 2007. &#8220;The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration.&#8221; <em>Nature Biotechnology</em> 25 (11): 1251&#8211;5. doi:<a href="https://doi.org/10.1038/nbt1346">10.1038/nbt1346</a>.</p>
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</div>
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<div id="ref-OWLAPI">
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<p>&#8220;The OWL API.&#8221; n.d. <a href="http://owlapi.sourceforge.net/" class="uri">http://owlapi.sourceforge.net/</a>. <a href="http://owlapi.sourceforge.net/" class="uri">http://owlapi.sourceforge.net/</a>.</p>
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</div>
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<div id="ref-OWL2009">
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<p>W3C OWL Working Group. 2009. &#8220;OWL 2 Web Ontology Language Document Overview.&#8221; <a href="https://www.w3.org/TR/owl2-overview/" class="uri">https://www.w3.org/TR/owl2-overview/</a>. <a href="https://www.w3.org/TR/owl2-overview/" class="uri">https://www.w3.org/TR/owl2-overview/</a>.</p>
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</div>
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</div>
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</div>
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</div>
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EOF

‎joss.00023/10.21105.joss.00023.pdf

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‎joss.00023/10.21105.joss.00023.xml

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<?xml version="1.0" encoding="utf-8" ?>
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<article>
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<articleinfo>
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<title>Scowl: a Scala DSL for programming with the OWL API</title>
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<authors>
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<author>
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<name>James P Balhoff</name>
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<orcid>0000-0002-8688-6599</orcid>
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<affiliation>
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<orgname>
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RTI International
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</orgname>
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</affiliation>
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</author>
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</authors>
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<tags>
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<tag>OWL</tag>
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<tag>ontology</tag>
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</tags>
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<date>17 May 2016</date>
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<paper_doi>10.21105/joss.00023</paper_doi>
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<software_repository>https://github.com/phenoscape/scowl</software_repository>
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<software_archive>http://dx.doi.org/10.5281/zenodo.51556</software_archive>
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<paper_url>https://github.com/openjournals/joss-papers/blob/master/joss.00023/10.21105.joss.00023.pdf</paper_url>
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</articleinfo>
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<body>
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<h1 id="summary">Summary</h1>
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<p>Scowl is a domain-specific language (DSL) which provides a convenient Scala-based syntax for composing OWL (Web Ontology Language, <span class="citation">(W3C OWL Working Group 2009)</span>) expressions and axioms. Effective use of complex, community developed ontologies within research applications, such as those from the OBO library (Open Biomedical Ontologies, <span class="citation">(Smith et al. 2007)</span>), often requires custom programmatic manipulation of ontologies and data, along with input to and output from automated reasoners. Allowing deeply nested OWL constructs to be coded in a readable, declarative style, Scowl facilitates use cases at the interface of application programming and OWL modeling: 1) tabular data ingest and transformation into OWL; 2) ontology manipulation via programmatic generation of axioms from existing content; and 3) reporting on ontology content using pattern matching on OWL objects.</p>
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<p>Within Scala applications, Scowl adds extension methods to native Java OWL API objects <span class="citation">(“The OWL API,” n.d.)</span>, supporting two syntax styles: the pseudo-English Manchester syntax <span class="citation">(Horridge and Patel-Schneider 2009)</span>, as well as the OWL Functional syntax <span class="citation">(Motik et al. 2009)</span>. Integration with the standard Java OWL API provides compatibility with multiple freely available OWL reasoners.</p>
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<h1 id="references" class="unnumbered">References</h1>
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<div id="refs" class="references">
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<div id="ref-Horridge2009">
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<p>Horridge, Matthew, and Peter F Patel-Schneider. 2009. “OWL 2 Web Ontology Language Manchester Syntax.” <a href="https://www.w3.org/TR/owl2-manchester-syntax/" class="uri">https://www.w3.org/TR/owl2-manchester-syntax/</a>. <a href="https://www.w3.org/TR/owl2-manchester-syntax/" class="uri">https://www.w3.org/TR/owl2-manchester-syntax/</a>.</p>
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</div>
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<div id="ref-Motik2009">
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<p>Motik, Boris, Peter F Patel-Schneider, Bijan Parsia, Conrad Bock, Achille Fokoue, Peter Haase, Rinke Hoekstra, Ian Horrocks, Alan Ruttenberg, and Uli Sattler. 2009. “OWL 2 Web Ontology Language: Structural Specification and Functional-Style Syntax.” <a href="https://www.w3.org/TR/owl2-syntax/" class="uri">https://www.w3.org/TR/owl2-syntax/</a>. <a href="https://www.w3.org/TR/owl2-syntax/" class="uri">https://www.w3.org/TR/owl2-syntax/</a>.</p>
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</div>
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<div id="ref-Smith2007">
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<p>Smith, Barry, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J Goldberg, et al. 2007. “The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration.” <em>Nature Biotechnology</em> 25 (11): 1251–5. doi:<a href="https://doi.org/10.1038/nbt1346">10.1038/nbt1346</a>.</p>
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</div>
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<div id="ref-OWLAPI">
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<p>“The OWL API.” n.d. <a href="http://owlapi.sourceforge.net/" class="uri">http://owlapi.sourceforge.net/</a>. <a href="http://owlapi.sourceforge.net/" class="uri">http://owlapi.sourceforge.net/</a>.</p>
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</div>
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<div id="ref-OWL2009">
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<p>W3C OWL Working Group. 2009. “OWL 2 Web Ontology Language Document Overview.” <a href="https://www.w3.org/TR/owl2-overview/" class="uri">https://www.w3.org/TR/owl2-overview/</a>. <a href="https://www.w3.org/TR/owl2-overview/" class="uri">https://www.w3.org/TR/owl2-overview/</a>.</p>
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</div>
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</div>
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</body>
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</article>

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