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10.21105.joss.00023.jats
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<?xml version="1.0" encoding="utf-8" ?>
<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Publishing DTD v1.2 20190208//EN"
"JATS-publishing1.dtd">
<article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" dtd-version="1.2" article-type="other">
<front>
<journal-meta>
<journal-id></journal-id>
<journal-title-group>
<journal-title>Journal of Open Source Software</journal-title>
<abbrev-journal-title>JOSS</abbrev-journal-title>
</journal-title-group>
<issn publication-format="electronic">2475-9066</issn>
<publisher>
<publisher-name>Open Journals</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="publisher-id">23</article-id>
<article-id pub-id-type="doi">10.21105/joss.00023</article-id>
<title-group>
<article-title>Scowl: a Scala DSL for programming with the OWL
API</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<contrib-id contrib-id-type="orcid">0000-0002-8688-6599</contrib-id>
<string-name>James P Balhoff</string-name>
<xref ref-type="aff" rid="aff-1"/>
</contrib>
<aff id="aff-1">
<institution-wrap>
<institution>RTI International</institution>
</institution-wrap>
</aff>
</contrib-group>
<pub-date date-type="pub" publication-format="electronic" iso-8601-date="2016-05-17">
<day>17</day>
<month>5</month>
<year>2016</year>
</pub-date>
<volume>1</volume>
<issue>1</issue>
<fpage>23</fpage>
<permissions>
<copyright-statement>Authors of papers retain copyright and release the
work under a Creative Commons Attribution 4.0 International License (CC
BY 4.0)</copyright-statement>
<copyright-year>2021</copyright-year>
<copyright-holder>The article authors</copyright-holder>
<license license-type="open-access" xlink:href="https://creativecommons.org/licenses/by/4.0/">
<license-p>Authors of papers retain copyright and release the work under
a Creative Commons Attribution 4.0 International License (CC BY
4.0)</license-p>
</license>
</permissions>
<kwd-group kwd-group-type="author">
<kwd>OWL</kwd>
<kwd>ontology</kwd>
</kwd-group>
</article-meta>
</front>
<body>
<sec id="summary">
<title>Summary</title>
<p>Scowl is a domain-specific language (DSL) which provides a
convenient Scala-based syntax for composing OWL (Web Ontology
Language,
(<xref alt="W3C OWL Working Group, 2009" rid="ref-OWL2009" ref-type="bibr">W3C
OWL Working Group, 2009</xref>)) expressions and axioms. Effective use
of complex, community developed ontologies within research
applications, such as those from the OBO library (Open Biomedical
Ontologies,
(<xref alt="Smith et al., 2007" rid="ref-Smith2007" ref-type="bibr">Smith
et al., 2007</xref>)), 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>
<p>Within Scala applications, Scowl adds extension methods to native
Java OWL API objects
(<xref alt="The OWL API, n.d." rid="ref-OWLAPI" ref-type="bibr"><italic>The
OWL API</italic>, n.d.</xref>), supporting two syntax styles: the
pseudo-English Manchester syntax
(<xref alt="Horridge & Patel-Schneider, 2009" rid="ref-Horridge2009" ref-type="bibr">Horridge
& Patel-Schneider, 2009</xref>), as well as the OWL Functional
syntax
(<xref alt="Motik et al., 2009" rid="ref-Motik2009" ref-type="bibr">Motik
et al., 2009</xref>). Integration with the standard Java OWL API
provides compatibility with multiple freely available OWL
reasoners.</p>
</sec>
</body>
<back>
<ref-list>
<ref-list>
<ref id="ref-OWLAPI">
<element-citation publication-type="webpage">
<article-title>The OWL API</article-title>
<uri>http://owlapi.sourceforge.net/</uri>
</element-citation>
</ref>
<ref id="ref-Horridge2009">
<element-citation publication-type="webpage">
<person-group person-group-type="author">
<name><surname>Horridge</surname><given-names>Matthew</given-names></name>
<name><surname>Patel-Schneider</surname><given-names>Peter F</given-names></name>
</person-group>
<article-title>OWL 2 web ontology language manchester syntax</article-title>
<year iso-8601-date="2009">2009</year>
<uri>https://www.w3.org/TR/owl2-manchester-syntax/</uri>
</element-citation>
</ref>
<ref id="ref-Motik2009">
<element-citation publication-type="webpage">
<person-group person-group-type="author">
<name><surname>Motik</surname><given-names>Boris</given-names></name>
<name><surname>Patel-Schneider</surname><given-names>Peter F</given-names></name>
<name><surname>Parsia</surname><given-names>Bijan</given-names></name>
<name><surname>Bock</surname><given-names>Conrad</given-names></name>
<name><surname>Fokoue</surname><given-names>Achille</given-names></name>
<name><surname>Haase</surname><given-names>Peter</given-names></name>
<name><surname>Hoekstra</surname><given-names>Rinke</given-names></name>
<name><surname>Horrocks</surname><given-names>Ian</given-names></name>
<name><surname>Ruttenberg</surname><given-names>Alan</given-names></name>
<name><surname>Sattler</surname><given-names>Uli</given-names></name>
</person-group>
<article-title>OWL 2 web ontology language: Structural specification and functional-style syntax</article-title>
<year iso-8601-date="2009">2009</year>
<uri>https://www.w3.org/TR/owl2-syntax/</uri>
</element-citation>
</ref>
<ref id="ref-OWL2009">
<element-citation publication-type="webpage">
<person-group person-group-type="author">
<string-name>W3C OWL Working Group</string-name>
</person-group>
<article-title>OWL 2 web ontology language document overview</article-title>
<year iso-8601-date="2009">2009</year>
<uri>https://www.w3.org/TR/owl2-overview/</uri>
</element-citation>
</ref>
<ref id="ref-Smith2007">
<element-citation publication-type="article-journal">
<person-group person-group-type="author">
<name><surname>Smith</surname><given-names>Barry</given-names></name>
<name><surname>Ashburner</surname><given-names>Michael</given-names></name>
<name><surname>Rosse</surname><given-names>Cornelius</given-names></name>
<name><surname>Bard</surname><given-names>Jonathan</given-names></name>
<name><surname>Bug</surname><given-names>William</given-names></name>
<name><surname>Ceusters</surname><given-names>Werner</given-names></name>
<name><surname>Goldberg</surname><given-names>Louis J</given-names></name>
<name><surname>Eilbeck</surname><given-names>Karen</given-names></name>
<name><surname>Ireland</surname><given-names>Amelia</given-names></name>
<name><surname>Mungall</surname><given-names>Christopher J</given-names></name>
<string-name>OBI Consortium</string-name>
<name><surname>Leontis</surname><given-names>Neocles</given-names></name>
<name><surname>Rocca-Serra</surname><given-names>Philippe</given-names></name>
<name><surname>Ruttenberg</surname><given-names>Alan</given-names></name>
<name><surname>Sansone</surname><given-names>Susanna-Assunta</given-names></name>
<name><surname>Scheuermann</surname><given-names>Richard H</given-names></name>
<name><surname>Shah</surname><given-names>Nigam</given-names></name>
<name><surname>Whetzel</surname><given-names>Patricia L</given-names></name>
<name><surname>Lewis</surname><given-names>Suzanna</given-names></name>
</person-group>
<article-title>The OBO foundry: Coordinated evolution of ontologies to support biomedical data integration</article-title>
<source>Nature biotechnology</source>
<year iso-8601-date="2007-11">2007</year><month>11</month>
<volume>25</volume>
<issue>11</issue>
<issn>1087-0156</issn>
<uri>http://dx.doi.org/10.1038/nbt1346</uri>
<pub-id pub-id-type="doi">10.1038/nbt1346</pub-id>
<pub-id pub-id-type="pmid">17989687</pub-id>
</element-citation>
</ref>
</ref-list>
</ref-list>
</back>
</article>