ontoCAT: an R package for ontology traversal and search | Bioinformatics

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Biotechnol.; citation_year=2007; citation_volume=25; citation_pages=1251-1255; " /><meta name="citation_reference" content="citation_title=Integration of biological networks and gene expression data using Cytoscape; Nat. Protocol.; citation_year=2007; citation_volume=2; citation_pages=2366-2382; " /><meta name="citation_reference" content="citation_title=The ontology lookup service: more data and better tools for controlled vocabulary queries; Nucleic Acids Res.; citation_year=2008; citation_volume=36; citation_issue=Suppl. 2; citation_pages=W372-W376; " /><meta name="citation_reference" content="citation_publisher=Chapman & Hall\CRC, ; R Programming for Bioinformatics.; citation_year=2008; " /><meta name="citation_reference" content="citation_title=The OWL API: a Java API for working with OWL 2 ontologies; citation_publisher=Chantilly, Virginia; OWLED 2009, 6th OWL Experienced and Directions Workshop.; citation_year=2009; " /><meta name="citation_reference" content="citation_publisher=Trafford Publishing, Victoria, BC; OWL: representing Information Using the Web Ontology Language.; citation_year=2005; " /><meta name="citation_reference" content="citation_title=Hypertableau reasoning for description logics; J. 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class="article-issue-info"> <div class="volume-issue__wrap"> <div class="volume trailing-comma">Volume 27</div> <div class="issue">Issue 17</div> </div> <div class="ii-pub-date"> September 2011 </div> </div> </a> </div> </div> <div class="content-nav"> <div class="widget widget-ArticleJumpLinks widget-instance-OUP_ArticleJumpLinks_Widget"> <h3 class="contents-title" >Article Contents</h3> <ul class="jumplink-list js-jumplink-list"> <li class="section-jump-link head-1" link-destination="393604558"> <div class="section-jump-link__link-wrap"> <a class="js-jumplink scrollTo" href="#393604558">Abstract</a> </div> </li> <li class="section-jump-link head-1" link-destination="393604559"> <div class="section-jump-link__link-wrap"> <a class="js-jumplink scrollTo" href="#393604559">1 INTRODUCTION</a> </div> </li> <li class="section-jump-link head-1" link-destination="393604568"> <div class="section-jump-link__link-wrap"> <a class="js-jumplink scrollTo" href="#393604568">2 METHODS</a> </div> </li> <li class="section-jump-link head-1" link-destination="393604594"> <div class="section-jump-link__link-wrap"> <a class="js-jumplink scrollTo" href="#393604594">3 TECHNICAL DETAILS</a> </div> </li> <li class="section-jump-link head-1" link-destination="393604600"> <div class="section-jump-link__link-wrap"> <a class="js-jumplink scrollTo" href="#393604600">4 CONCLUSION</a> </div> </li> <li class="section-jump-link head-1" link-destination="393604603"> <div class="section-jump-link__link-wrap"> <a class="js-jumplink scrollTo" href="#393604603">ACKNOWLEDGEMENT</a> </div> </li> <li class="section-jump-link head-1 backReferenceLink" link-destination="393604607"> <div class="section-jump-link__link-wrap"> <a class="js-jumplink scrollTo" href="#393604607">REFERENCES</a> </div> </li> </ul> </div> </div> <div class="widget widget-ArticleNavLinks widget-instance-OUP_ArticleNavLinks_Article"> <ul class="inline-list"> <li class="prev arrow"> <a href="/bioinformatics/article/27/17/2465/224780">< 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class="journal-info__format-label">Journal Article</span> </div> <div class="widget-items"> <div class="title-wrap"> <h1 class="wi-article-title article-title-main accessible-content-title at-articleTitle"> <span class="monospace">ontoCAT</span>: an <span class="sans-serif">R</span> package for ontology traversal and search <i class='icon-availability_free' title='Free' ></i> </h1> </div> <div class="wi-authors at-ArticleAuthors"> <div class="al-authors-list"> <span class="al-author-name-more js-flyout-wrap"> <button type="button" class="linked-name js-linked-name-trigger btn-as-link">Natalja Kurbatova</button><span class='delimiter'>, </span> <span class="al-author-info-wrap arrow-up"> <div class="info-card-author authorInfo_OUP_ArticleTop_Info_Widget"> <div class="name-role-wrap"> <div class="info-card-name"> Natalja Kurbatova <span class="info-card-footnote"><span class="xrefLink" id="jumplink-COR1"></span><a href="javascript:;" reveal-id="COR1" data-open="COR1" class="link link-ref link-reveal xref-default"><sup>*</sup></a></span> </div> </div> <div class="info-card-affilitation"> <div class="aff"><span class="label title-label"><sup>1</sup></span>EMBL Outstation-Hinxton, European Bioinformatics Institute, Cambridge, UK and <sup>2</sup>Genomics Coordination Center, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands</div> </div> <div class="info-author-correspondence"> <div content-id="COR1">* To whom correspondence should be addressed.</div> </div> <div class="info-card-search-label"> Search for other works by this author on: </div> <div class="info-card-search info-card-search-internal"> <a href="/bioinformatics/search-results?f_Authors=Natalja+Kurbatova" rel="nofollow">Oxford Academic</a> </div> <div class="info-card-search info-card-search-pubmed"> <a href="http://www.ncbi.nlm.nih.gov/pubmed?cmd=search&term=Kurbatova N">PubMed</a> </div> <div class="info-card-search info-card-search-google"> <a href="http://scholar.google.com/scholar?q=author:%22Kurbatova Natalja%22">Google Scholar</a> </div> </div> </span> </span> <span class="al-author-name-more js-flyout-wrap"> <button type="button" class="linked-name js-linked-name-trigger btn-as-link">Tomasz Adamusiak</button><span class='delimiter'>, </span> <span class="al-author-info-wrap arrow-up"> <div class="info-card-author authorInfo_OUP_ArticleTop_Info_Widget"> <div class="name-role-wrap"> <div class="info-card-name"> Tomasz Adamusiak </div> </div> <div class="info-card-affilitation"> <div class="aff"><span class="label title-label"><sup>1</sup></span>EMBL Outstation-Hinxton, European Bioinformatics Institute, Cambridge, UK and <sup>2</sup>Genomics Coordination Center, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands</div> </div> <div class="info-card-search-label"> Search for other works by this author on: </div> <div class="info-card-search info-card-search-internal"> <a href="/bioinformatics/search-results?f_Authors=Tomasz+Adamusiak" rel="nofollow">Oxford Academic</a> </div> <div class="info-card-search info-card-search-pubmed"> <a href="http://www.ncbi.nlm.nih.gov/pubmed?cmd=search&term=Adamusiak T">PubMed</a> </div> <div class="info-card-search info-card-search-google"> <a href="http://scholar.google.com/scholar?q=author:%22Adamusiak Tomasz%22">Google Scholar</a> </div> </div> </span> </span> <span class="al-author-name-more js-flyout-wrap"> <button type="button" class="linked-name js-linked-name-trigger btn-as-link">Pavel Kurnosov</button><span class='delimiter'>, </span> <span class="al-author-info-wrap arrow-up"> <div class="info-card-author authorInfo_OUP_ArticleTop_Info_Widget"> <div class="name-role-wrap"> <div class="info-card-name"> Pavel Kurnosov </div> </div> <div class="info-card-affilitation"> <div class="aff"><span class="label title-label"><sup>1</sup></span>EMBL Outstation-Hinxton, European Bioinformatics Institute, Cambridge, UK and <sup>2</sup>Genomics Coordination Center, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands</div> </div> <div class="info-card-search-label"> Search for other works by this author on: </div> <div class="info-card-search info-card-search-internal"> <a href="/bioinformatics/search-results?f_Authors=Pavel+Kurnosov" rel="nofollow">Oxford Academic</a> </div> <div class="info-card-search info-card-search-pubmed"> <a href="http://www.ncbi.nlm.nih.gov/pubmed?cmd=search&term=Kurnosov P">PubMed</a> </div> <div class="info-card-search info-card-search-google"> <a href="http://scholar.google.com/scholar?q=author:%22Kurnosov Pavel%22">Google Scholar</a> </div> </div> </span> </span> <span class="al-author-name-more js-flyout-wrap"> <button type="button" class="linked-name js-linked-name-trigger btn-as-link">Morris A. Swertz</button><span class='delimiter'>, </span> <span class="al-author-info-wrap arrow-up"> <div class="info-card-author authorInfo_OUP_ArticleTop_Info_Widget"> <div class="name-role-wrap"> <div class="info-card-name"> Morris A. Swertz </div> </div> <div class="info-card-affilitation"> <div class="aff"><span class="label title-label"><sup>1</sup></span>EMBL Outstation-Hinxton, European Bioinformatics Institute, Cambridge, UK and <sup>2</sup>Genomics Coordination Center, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands</div><div class="aff"><span class="label title-label"><sup>1</sup></span>EMBL Outstation-Hinxton, European Bioinformatics Institute, Cambridge, UK and <sup>2</sup>Genomics Coordination Center, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands</div> </div> <div class="info-card-search-label"> Search for other works by this author on: </div> <div class="info-card-search info-card-search-internal"> <a href="/bioinformatics/search-results?f_Authors=Morris+A.+Swertz" rel="nofollow">Oxford Academic</a> </div> <div class="info-card-search info-card-search-pubmed"> <a href="http://www.ncbi.nlm.nih.gov/pubmed?cmd=search&term=Swertz M">PubMed</a> </div> <div class="info-card-search info-card-search-google"> <a href="http://scholar.google.com/scholar?q=author:%22Swertz Morris A.%22">Google Scholar</a> </div> </div> </span> </span> <span class="al-author-name-more js-flyout-wrap"> <button type="button" class="linked-name js-linked-name-trigger btn-as-link">Misha Kapushesky</button><span class='delimiter'></span> <span class="al-author-info-wrap arrow-up"> <div class="info-card-author authorInfo_OUP_ArticleTop_Info_Widget"> <div class="name-role-wrap"> <div class="info-card-name"> Misha Kapushesky </div> </div> <div class="info-card-affilitation"> <div class="aff"><span class="label title-label"><sup>1</sup></span>EMBL Outstation-Hinxton, European Bioinformatics Institute, Cambridge, UK and <sup>2</sup>Genomics Coordination Center, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands</div> </div> <div class="info-card-search-label"> Search for other works by this author on: </div> <div class="info-card-search info-card-search-internal"> <a href="/bioinformatics/search-results?f_Authors=Misha+Kapushesky" rel="nofollow">Oxford Academic</a> </div> <div class="info-card-search info-card-search-pubmed"> <a href="http://www.ncbi.nlm.nih.gov/pubmed?cmd=search&term=Kapushesky M">PubMed</a> </div> <div class="info-card-search info-card-search-google"> <a href="http://scholar.google.com/scholar?q=author:%22Kapushesky Misha%22">Google Scholar</a> </div> </div> </span> </span> <div class="al-author-name al-author-footnotes"> <div class="al-author-info-wrap arrow-up"> <div class="widget widget-SingleSection widget-instance-OUP_FootnoteSection"> <div content-id="" class="footnote"><span class="fn"><div class="footnote-content"><p class="footnote-compatibility">Associate Editor: Alex Bateman</p></div></span></div> </div> </div> <a class="js-linked-footnotes" href="javascript:;">Author Notes</a> </div> </div> </div> <div class="pub-history-wrap clearfix js-history-dropdown-wrap"> <div class="pub-history-row clearfix"> <div class="ww-citation-primary"><em>Bioinformatics</em>, Volume 27, Issue 17, September 2011, Pages 2468–2470, <a href='https://doi.org/10.1093/bioinformatics/btr375'>https://doi.org/10.1093/bioinformatics/btr375</a></div> </div> <div class="pub-history-row clearfix"> <div class="ww-citation-date-wrap"> <div class="citation-label">Published:</div> <div class="citation-date">22 June 2011</div> </div> <a href="javascript:;" class="history-label js-history-dropdown-trigger st-article-history at-ArticleHistory"> <span>Article history</span><i class="icon-general-arrow-filled-down arrow-icon"></i> </a> </div> <div class="ww-history js-history-entries-wrap at-history-entries-wrap"> <div class="history-entry at-history-entry"> <div class="wi-state">Received:</div> <div class="wi-date">13 January 2011</div> </div> <div class="history-entry at-history-entry"> <div class="wi-state">Revision received:</div> <div class="wi-date">08 June 2011</div> </div> <div class="history-entry at-history-entry"> <div class="wi-state">Accepted:</div> <div class="wi-date">17 June 2011</div> </div> <div class="history-entry at-history-entry"> <div class="wi-state">Published:</div> <div class="wi-date">22 June 2011</div> </div> </div> </div> </div> </div> <script> $(document).ready(function () { $('.article-top-widget').on('click', '.ati-toggle-trigger', function () { $(this).find('.icon-general-add, .icon-minus').toggleClass('icon-minus icon-general-add'); 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>Abstract</h2> <section class="abstract"><p class="chapter-para"><strong>Motivation:</strong> There exist few simple and easily accessible methods to integrate ontologies programmatically in the <span class="sans-serif">R</span> environment. We present <span class="monospace">ontoCAT</span>—an <span class="sans-serif">R</span> package to access ontologies in widely used standard formats, stored locally in the filesystem or available online. The <span class="monospace">ontoCAT</span> package supports a number of traversal and search functions on a single ontology, as well as searching for ontology terms across multiple ontologies and in major ontology repositories.</p><p class="chapter-para"><strong>Availability:</strong> The package and sources are freely available in Bioconductor starting from version 2.8: <a class="link link-uri openInAnotherWindow" href="http://bioconductor.org/help/bioc-views/release/bioc/html/ontoCAT.html" target="_blank">http://bioconductor.org/help/bioc-views/release/bioc/html/ontoCAT.html</a> or via the OntoCAT website <a class="link link-uri openInAnotherWindow" href="http://www.ontocat.org/wiki/r" target="_blank">http://www.ontocat.org/wiki/r</a>.</p><p class="chapter-para"><strong>Contact:</strong> <a href="mailto:natalja@ebi.ac.uk" target="_blank">natalja@ebi.ac.uk</a>; <a href="mailto:natalja@ebi.ac.uk" target="_blank">natalja@ebi.ac.uk</a></p></section> <div class="article-metadata-panel clearfix at-ArticleMetadata"></div> <h2 scrollto-destination=393604559 id="393604559" class="section-title js-splitscreen-section-title" data-legacy-id=SEC1>1 INTRODUCTION</h2> <p class="chapter-para">The <span class="sans-serif">R</span> package <span class="monospace">ontoCAT</span> was created to support basic operations on ontologies: traversal and search, uniform access to ontologies in OWL (<span class="xrefLink" id="jumplink-B8"></span><a href="javascript:;" reveal-id="B8" data-open="B8" class="link link-ref link-reveal xref-bibr">Lacy, 2005</a>) and OBO (<span class="xrefLink" id="jumplink-B3"></span><a href="javascript:;" reveal-id="B3" data-open="B3" class="link link-ref link-reveal xref-bibr">Barry <em>et al.</em>, 2007</a>) formats and to provide <span class="sans-serif">R</span> access to major ontology repositories OLS and BioPortal.</p><p class="chapter-para">Several hundreds of public ontologies and numerous private ontologies for describing biological data exist today. Using ontologies in <span class="sans-serif">R</span> (<span class="xrefLink" id="jumplink-B6"></span><a href="javascript:;" reveal-id="B6" data-open="B6" class="link link-ref link-reveal xref-bibr">Gentleman, 2008</a>; <span class="xrefLink" id="jumplink-B12"></span><a href="javascript:;" reveal-id="B12" data-open="B12" class="link link-ref link-reveal xref-bibr">R Development Core Team, 2006</a>) is difficult due to the lack of uniform package support. At the same time numerous Java-based ontology projects are available. <span class="monospace">ontoCAT</span> takes advantage of a standard Java library with the same name ‘ontoCAT’ (<span class="xrefLink" id="jumplink-B1"></span><a href="javascript:;" reveal-id="B1" data-open="B1" class="link link-ref link-reveal xref-bibr">Adamusiak <em>et al.</em>, 2010</a>, <span class="xrefLink" id="jumplink-B2"></span><a href="javascript:;" reveal-id="B2" data-open="B2" class="link link-ref link-reveal xref-bibr">2011</a>) to implement its functionality.</p><p class="chapter-para">The <span class="monospace">ontoCAT</span> package: </p><ul class="bullet"><li><p class="chapter-para">gives unified, format-independent access to ontology terms and the ontology hierarchy represented in OWL and OBO formats;</p></li><li><p class="chapter-para">provides basic methods for ontology traversal, such as searching for terms, listing a specific term's relations, showing paths to the term from the root element of the ontology, showing flattened-tree representations of the ontology hierarchy; and</p></li><li><p class="chapter-para">supports working with groups of ontologies and with major public ontology repositories: searching for terms across ontologies, listing available ontologies and loading ontologies for further analysis as necessary.</p></li></ul><p class="chapter-para">No other package with similar functionality exists at the moment in the <span class="sans-serif">R</span> environment.</p><p class="chapter-para">The integration of the above functionality into <span class="sans-serif">R</span> allows combining and automating ontology-related tasks. Different examples of ontology-related tasks that can be accomplished with the help of the <span class="monospace">ontoCAT</span> package are given in the package documentation (<a class="link link-uri openInAnotherWindow" href="http://www.ontocat.org/wiki/OntocatGuide" target="_blank">http://www.ontocat.org/wiki/OntocatGuide</a>): gene enrichment test and grouping of results, search and re-annotation of free-text to ontology and operations with relationships.</p><p class="chapter-para"><span class="monospace">ontoCAT</span> has been included into Bioconductor, the main <span class="sans-serif">R</span> open source project in bioinformatics. <span class="monospace">ontoCAT</span> has been downloaded 347 times since its first release in December 2010.</p><p class="chapter-para">There is a large research community already using <span class="sans-serif">R</span> to work with Gene Ontology (GO). Working with other ontologies is not as well–developed and <span class="monospace">ontoCAT</span> helps to fill the gap.</p> <h2 scrollto-destination=393604568 id="393604568" class="section-title js-splitscreen-section-title" data-legacy-id=SEC2>2 METHODS</h2> <p class="chapter-para">The <span class="monospace">ontoCAT</span><span class="sans-serif">R</span> package consists of two main parts, grouping similar methods: </p><ul class="bullet"><li><p class="chapter-para">Single ontology traversal methods.</p></li><li><p class="chapter-para">Methods to work across multiple ontologies.</p></li></ul> <h3 scrollto-destination=393604571 id="393604571" class="section-title js-splitscreen-section-title" data-legacy-id=SEC2.1>2.1 Single ontology traversal methods</h3> <p class="chapter-para">The <span class="monospace">ontoCAT</span> package can load an ontology in OWL or OBO format from a local file or on-the-fly from a URI.</p><p class="chapter-para">Reasoning over ontologies and extracting relationships is supported by using HermiT (<span class="xrefLink" id="jumplink-B9"></span><a href="javascript:;" reveal-id="B9" data-open="B9" class="link link-ref link-reveal xref-bibr">Motik <em>et al.</em>, 2009</a>) reasoner. OBO ontologies are translated by OWL API (<span class="xrefLink" id="jumplink-B7"></span><a href="javascript:;" reveal-id="B7" data-open="B7" class="link link-ref link-reveal xref-bibr">Horridge and Bechhofer, 2009</a>) into valid OWL format that can be reasoned over.</p><p class="chapter-para">Ontologies can also be loaded from ontology repositories. Two public repositories are supported: BioPortal for accessing and sharing biomedical ontologies (<span class="xrefLink" id="jumplink-B10"></span><a href="javascript:;" reveal-id="B10" data-open="B10" class="link link-ref link-reveal xref-bibr">Noy <em>et al.</em>, 2009</a>), currently hosting 241 ontologies and the Ontology Lookup Service (OLS) for querying multiple ontologies (<span class="xrefLink" id="jumplink-B5"></span><a href="javascript:;" reveal-id="B5" data-open="B5" class="link link-ref link-reveal xref-bibr">Cote <em>et al.</em>, 2008</a>), currently hosting 81 ontologies.</p><p class="chapter-para">To load an ontology <span class="monospace">getOntology(path/accession)</span> method of the <span class="monospace">Ontology</span> class is available. It takes a single argument, specifying the local filesystem path, the full URI for the ontology file, or its OLS/BioPortal accession.</p><p class="chapter-para">The reference ontology supported by <span class="monospace">ontoCAT</span> is Experimental Factor Ontology (EFO) (<span class="xrefLink" id="jumplink-B11"></span><a href="javascript:;" reveal-id="B11" data-open="B11" class="link link-ref link-reveal xref-bibr">Malone <em>et al.</em>, 2010</a>), developed for applications in functional genomics. The latest version of EFO can be loaded by using the method <span class="monospace">getEFO()</span>.</p><p class="chapter-para">When an ontology is loaded, other <span class="monospace">ontoCAT</span> methods become available.</p><p class="chapter-para">In <span class="monospace">ontoCAT</span> the subsumption ‘subclass/superclass’ is supported in a user friendly form of ‘child – parent’ relationship.</p><p class="chapter-para">No distinction is made between universals (classes) and particulars (instances) as they are both treated as ontology terms with parent–child relationship: class is treated as parent, instances are children of the class.</p><p class="chapter-para">The advantage of using a reasoner in <span class="monospace">ontoCAT</span> is the ability to work with different relationships in addition to subsumption. However, if reasoning over ontology is not desirable <span class="monospace">getOntologyNoReasoning</span> method should be used instead of <span class="monospace">getOntology</span> method described above.</p><p class="chapter-para">An example of relationships that can be retrieved by <span class="monospace">ontoCAT</span> starting from a particular EFO ontology term ‘EFO_0000815’ (heart) is given in <span class="xrefLink" id="jumplink-F1"></span><a href="javascript:;" data-modal-source-id="F1" class="link xref-fig">Figure 1</a>. </p> <a id="393604582" scrollto-destination="393604582"></a> <div data-id="f1" data-content-id="f1" class="fig fig-section js-fig-section" swap-content-for-modal="true"><div class="graphic-wrap"><img class="content-image" src="https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/bioinformatics/27/17/10.1093_bioinformatics_btr375/1/m_bioinformatics_27_17_2468_f1.jpeg?Expires=1734755794&Signature=cYN-BSdHXadpjFYhVDTTeBmLV8NKmoLwx5F75PFNPhyP13drK0a8HrYJHpOx8Uc4Tcz35jH~HIEgUpiM382D6o-reF4skqpgEVJtePOlpwSWbh5QCncMWJOr4wx0h9XElC9FGHahAALC0zeQtgh90nWAId2Ep2LTfIgpI-3XvAmMvPE3zPrF0cYt6WdMFEC9yv3SbgPkzfP8uIBl-oFUKFhbxnUVGCsg-0-010AX4XEStOpLlT52IfEU-nQP3NPv~hfwTqda8bnov1MKc9BxDBQ0N6Q71eQnX5SncR1Fi4bjDbp~LwLOjqxnY~xfKe~qvhlvtPq5OG-OzgVuIMo1dw__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA" alt="An example of a directed acyclic graph representing all the relationships in an ontology for a particular EFO ontology term ‘EFO_0000815’ (heart). Edges are labeled according to the relationship. Organism part classes are represented as ellipses and disease classes are shown as rectangles. The ontoCAT package was used to compute the relationships which were later processed in Cytoscape (Cline et al., 2007)." data-path-from-xml="BIOINFORMATICS_27_17_2468_f1.jpeg" /><div class="graphic-bottom"><div class="label fig-label" id="label-393604582">Fig. 1.</div><div class="caption fig-caption"><p class="chapter-para">An example of a directed acyclic graph representing all the relationships in an ontology for a particular EFO ontology term ‘EFO_0000815’ (heart). Edges are labeled according to the relationship. Organism part classes are represented as ellipses and disease classes are shown as rectangles. The <span class="monospace">ontoCAT</span> package was used to compute the relationships which were later processed in Cytoscape (<span class="xrefLink" id="jumplink-B4"></span><a href="javascript:;" reveal-id="B4" data-open="B4" class="link link-ref link-reveal xref-bibr">Cline <em>et al.</em>, 2007</a>).</p></div><div class="ajax-articleAbstract-exclude-regex fig-orig original-slide figure-button-wrap"><a class="fig-view-orig js-view-large at-figureViewLarge openInAnotherWindow" role="button" aria-describedby="label-393604582" href="/view-large/figure/393604582/BIOINFORMATICS_27_17_2468_f1.jpeg" data-path-from-xml="BIOINFORMATICS_27_17_2468_f1.jpeg" target="_blank">Open in new tab</a><a class="download-slide" role="button" aria-describedby="label-393604582" data-section="393604582" href="/DownloadFile/DownloadImage.aspx?image=https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/bioinformatics/27/17/10.1093_bioinformatics_btr375/1/bioinformatics_27_17_2468_f1.jpeg?Expires=1734755794&Signature=KMhIsV8BntTln4ZJip7XSiEOc4mad422ZNH19HGYDkAbG3N28r8nVppz3uGXgnTbzvd1opTuyY-ecGa0gj7gmnGyg4PIg2a8XnYWo8sfRAI92IJZyEPbYQ3AWLf~YCw6h32PwOSlb9ke-PxlPQse1z2jsaoos7k5xcdTV45tze~9t89hh1ZKY8ZYj-n1P1H6Oc63vxHCyzBPV-OqJJK7Cu17s54zJqoJbd9gqlZrphk57FfcTHn~20PjcLe~jAgG6OevoOPFuwP1BygAaH1jmykdfsxOl4In6ZRZ~cISk4tQBh4ck49Q31awL2jp0W7Iq4~u2qUGzbj5~qCVZ1NznA__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA&sec=393604582&ar=223268&xsltPath=~/UI/app/XSLT&imagename=&siteId=5139" data-path-from-xml="BIOINFORMATICS_27_17_2468_f1.jpeg">Download slide</a></div></div></div></div><p class="chapter-para">Below there are several examples of <span class="monospace">ontoCAT</span> methods: </p><ul class="bullet"><li><p class="chapter-para"><span class="monospace">searchTerm(Ontology, ‘myocardium’)</span> returns a list of terms where ‘myocardium’ is mentioned;</p></li><li><p class="chapter-para"><span class="monospace">getTermParentsById(Ontology, ‘EFO_0003087’)</span> lists parents of the term ‘EFO_0003087’ (atrial myocardium): ‘EFO_0000819’ (myocardium) (see <span class="xrefLink" id="jumplink-F1"></span><a href="javascript:;" data-modal-source-id="F1" class="link xref-fig">Fig. 1</a>);</p></li><li><p class="chapter-para"><span class="monospace">getTermById(Ontology, ‘EFO_0000819’)</span> returns ontology term by its accession: ‘EFO_0000819’ (myocardium);</p></li><li><p class="chapter-para"><span class="monospace">getTermChildren(Ontology, term)</span> lists children of the term ‘EFO_0000819’ (myocardium): ‘EFO_0003087’ (atrial myocardium) and ‘EFO_0003088’ (ventricular myocardium) (see <span class="xrefLink" id="jumplink-F1"></span><a href="javascript:;" data-modal-source-id="F1" class="link xref-fig">Fig. 1</a>);</p></li><li><p class="chapter-para"><span class="monospace">showHierarchyDownToTerm(Ontology, ‘EFO_0000819’)</span> prints out a flattened-tree representation of the ontology from the root term down to ‘EFO_0000819’ (myocardium) by using parent–child relationships;</p></li><li><p class="chapter-para"><span class="monospace">getTermRelationsById(Ontology, ‘EFO_0000815’, ‘has_part’)</span> returns terms in relation ‘has_part’ with ‘EFO_0000815’ (heart): ‘EFO_0000277’ (atrium), ‘EFO_0000819’ (myocardium) and ‘EFO_0000317’ (cardiac ventricle) (see <span class="xrefLink" id="jumplink-F1"></span><a href="javascript:;" data-modal-source-id="F1" class="link xref-fig">Fig. 1</a>);</p></li><li><p class="chapter-para"><span class="monospace">getTermSynonyms(Ontology, term)</span> returns a list of synonyms for the term ‘EFO_0000819’ (myocardium): ‘muscle of heart’, ‘cardiac muscle’, ‘heart muscle’; and</p></li><li><p class="chapter-para"><span class="monospace">getRootTerms(Ontology)</span> returns a list of terms without parents in ontology of interest.</p></li></ul><p class="chapter-para">A number of self-descriptive methods like <span class="monospace">showPathsToTerm(Ontology, term)</span>, <span class="monospace">isRoot(Ontology, term)</span> are also available. The full list of methods together with descriptions is provided in online documentation (<a class="link link-uri openInAnotherWindow" href="http://www.ontocat.org/wiki/r" target="_blank">http://www.ontocat.org/wiki/r</a>) and is included into the package.</p> <h3 scrollto-destination=393604586 id="393604586" class="section-title js-splitscreen-section-title" data-legacy-id=SEC2.2>2.2 Operations on multiple ontologies</h3> <p class="chapter-para"><span class="monospace">ontoCAT</span> provides methods to work with groups or ‘batches’ of ontologies, local or web-based. Users can search for terms across such resources and load specific individual ontologies by accession.</p><p class="chapter-para">To create a local batch of ontologies the <span class="monospace">getOntologyBatch(path)</span> method of the <em>batch</em> class is provided, taking a single argument: the path to the local directory containing ontology files.</p><p class="chapter-para">By default, a call to <span class="monospace">getOntologyBatch()</span> without any arguments will load the EFO ontology. Ontologies can be added to an existing batch as needed via the <span class="monospace">addOntology()</span> method.</p><p class="chapter-para">After a batch of ontologies is created, various methods become available, including: </p><ul class="bullet"><li><p class="chapter-para"><span class="monospace">searchTerm(batch, ‘heart’)</span> searches for the term in all ontologies in the batch;</p></li><li><p class="chapter-para"><span class="monospace">searchTermInOLS(‘heart’)</span> searches for the term in OLS repository;</p></li><li><p class="chapter-para"><span class="monospace">searchTermInBioPortal(‘heart’)</span> searches for the term in BioPortal repository; and</p></li><li><p class="chapter-para"><span class="monospace">searchTermInAll(batch,‘heart’)</span> searches for the term in all ontologies in the batch as well as in OLS and BioPortal repositories.</p></li></ul><p class="chapter-para">The <span class="monospace">ontoCAT</span> package also provides methods to list ontologies in batches and to list ontologies available in BioPortal and OLS: <span class="monospace">listLoadedOntologies(batch)</span>, <span class="monospace">listOLSOntologies(batch)</span> and <span class="monospace">listBioportalOntologies(batch)</span>.</p><p class="chapter-para">When the sought terms are found and term-specific operations (parent/child/other relationships retrieval, etc.) are needed, the <span class="monospace">getOntology(batch,accession)</span> returns the ontology object for the concrete ontology with all single-ontology methods available.</p> <h2 scrollto-destination=393604594 id="393604594" class="section-title js-splitscreen-section-title" data-legacy-id=SEC3>3 TECHNICAL DETAILS</h2> <p class="chapter-para">The package is based primarily on the Ontology Common API Tasks Java library, on the OWL API and depends on <span class="monospace">rJava</span><span class="sans-serif">R</span> package. HermiT reasoner is used to support relationships.</p><p class="chapter-para"><span class="monospace">ontoCAT</span> <span class="sans-serif">R</span> package is open-source and is available under the Apache License Version 2.0.</p><p class="chapter-para">We provide two versions of <span class="monospace">ontoCAT</span>: </p><ul class="bullet"><li><p class="chapter-para">Light-weight <span class="monospace">ontoCAT</span> package version is available in Bioconductor (<a class="link link-uri openInAnotherWindow" href="http://bioconductor.org" target="_blank">http://bioconductor.org</a>) starting from release 2.7, and includes all single-ontology functionality except for methods to work with multiple ontologies and search in OLS and BioPortal.</p></li><li><p class="chapter-para">Full version includes batch methods and due to package size limitations are available only from the project website.</p></li></ul><p class="chapter-para">The package sources and full documentation are available at <a class="link link-uri openInAnotherWindow" href="http://www.ontocat.org/wiki/r" target="_blank">http://www.ontocat.org/wiki/r</a>.</p> <h2 scrollto-destination=393604600 id="393604600" class="section-title js-splitscreen-section-title" data-legacy-id=SEC4>4 CONCLUSION</h2> <p class="chapter-para">The <span class="monospace">ontoCAT</span><span class="sans-serif">R</span> package consists of convenient methods for working with ontologies in the <span class="sans-serif">R</span> environment. The package has been successfully used in a number of projects in the Functional Genomics Group at the European Bioinformatics Institute and this is its first public release.</p><p class="chapter-para">The package provides basic operations on ontologies represented in standard formats and enables searches in online ontology repositories: OLS and BioPortal.</p> <h2 scrollto-destination=393604603 id="393604603" class="backacknowledgements-title js-splitscreen-backacknowledgements-title" data-legacy-id=ack1>ACKNOWLEDGEMENT</h2> <p class="chapter-para">Ontology Common API Tasks development team and the EBI Gene Expression Atlas development team.</p><p class="chapter-para"><em>Funding</em>: European Community's Seventh Framework Programme projects GEN2PHEN (grant number 200754); SYBARIS (grant number 242220); NWO/Rubicon (grant number 825.09.008).</p><p class="chapter-para"><em>Conflict of Interest</em>: none declared.</p> <h2 scrollto-destination=393604607 id="393604607" class="backreferences-title js-splitscreen-backreferences-title" data-legacy-id=ref1>REFERENCES</h2> <div class="ref-list js-splitview-ref-list"><div content-id="B1" class="js-splitview-ref-item" data-legacy-id="B1"><div class="refLink-parent"><span class="refLink"><a name="jumplink-B1" href="javascript:;" aria-label="jumplink-B1" data-id=""></a></span></div><div class="ref false"><div id="ref-auto-B1" class="ref-content " data-id="B1"><div class="citation element-citation"><span class="person-group"><div class="name"><div class="surname">Adamusiak</div> <div class="given-names">T.</div></div>et al. </span><div class="article-title">OntoCAT – a simpler way to access ontology resources</div>, <div class="source ">Nature Precedings</div>, <div class="year">2010</div> <div class="comment">[Epub ahead of print; doi:10.1038/npre.2010.4666.1]</div><div class="citation-links"><p class="citation-links-compatibility"><span class="google-scholar-ref-link"><a class="openInAnotherWindow" href="https://scholar.google.com/scholar_lookup?title=OntoCAT%20%E2%80%93%20a%20simpler%20way%20to%20access%20ontology%20resources&author=T.%20Adamusiak&publication_year=2010&journal=Nature%20Precedings&volume=&pages=" target="_blank">Google Scholar</a></span></p><div class="xslopenurl empty-target"><span class="js-inst-open-url-holders-nodoi"><a class="js-open-url-link" data-href-template="{targetURL}?sid=oup:orr&genre=article&atitle=OntoCAT+%e2%80%93+a+simpler+way+to+access+ontology+resources&aulast=Adamusiak&title=Nature+Precedings&date=2010" href="javascript:;"><span class="screenreader-text">OpenURL Placeholder Text</span></a></span></div><p class="citation-links-compatibility"><span class="worldcat-reference-ref-link js-worldcat-preview-ref-link" style="display:none"><a class="openInAnotherWindow" href="https://www.worldcat.org/search?q=ti:OntoCAT%20%E2%80%93%20a%20simpler%20way%20to%20access%20ontology%20resources&qt=advanced&dblist=638" target="_blank">WorldCat</a></span></p> </div></div></div></div></div><div content-id="B2" class="js-splitview-ref-item" data-legacy-id="B2"><div class="refLink-parent"><span class="refLink"><a name="jumplink-B2" href="javascript:;" aria-label="jumplink-B2" data-id=""></a></span></div><div class="ref false"><div id="ref-auto-B2" class="ref-content " data-id="B2"><div class="citation element-citation"><span class="person-group"><div class="name"><div class="surname">Adamusiak</div> <div class="given-names">T.</div></div>et al. </span><div class="article-title">OntoCAT – simple ontology search and integration in Java, R and REST\JavaScript</div>, <div class="source ">BMC Bioinformatics</div>, <div class="year">2011</div>, vol. <div class="volume">12</div> pg. <div class="fpage">218</div> <div class="citation-links"></div><div class="citation-links"><p class="citation-links-compatibility"><span class="google-scholar-ref-link"><a class="openInAnotherWindow" href="https://scholar.google.com/scholar_lookup?title=OntoCAT%20%E2%80%93%20simple%20ontology%20search%20and%20integration%20in%20Java%2C%20R%20and%20REST%5CJavaScript&author=T.%20Adamusiak&publication_year=2011&journal=BMC%20Bioinformatics&volume=12&pages=218" target="_blank">Google Scholar</a></span></p><div class="crossref-doi js-ref-link"><a class="openInAnotherWindow" href="http://dx.doi.org/10.1186/1471-2105-12-218" target="_blank">Crossref</a></div><div class="adsDoiReference hide"><a class="openInAnotherWindow" href="http://adsabs.harvard.edu/cgi-bin/basic_connect?qsearch=10.1186%2F1471-2105-12-218" target="_blank">Search ADS</a></div><div class="xslopenurl empty-target"><span class="inst-open-url-holders" data-targetId="10.1186%2F1471-2105-12-218"> </span></div><div class="pub-id"><a href="http://www.ncbi.nlm.nih.gov/pubmed/21619703" class="link link-pub-id openInAnotherWindow" target="_blank">PubMed</a></div><p class="citation-links-compatibility"><span class="worldcat-reference-ref-link js-worldcat-preview-ref-link" style="display:none"><a class="openInAnotherWindow" href="https://www.worldcat.org/search?q=ti:OntoCAT%20%E2%80%93%20simple%20ontology%20search%20and%20integration%20in%20Java%2C%20R%20and%20REST%5CJavaScript&qt=advanced&dblist=638" target="_blank">WorldCat</a></span></p> </div></div></div></div></div><div content-id="B3" class="js-splitview-ref-item" data-legacy-id="B3"><div class="refLink-parent"><span class="refLink"><a name="jumplink-B3" href="javascript:;" aria-label="jumplink-B3" data-id=""></a></span></div><div class="ref false"><div id="ref-auto-B3" class="ref-content " data-id="B3"><div class="citation element-citation"><span class="person-group"><div class="name"><div class="surname">Barry</div> <div class="given-names">S.</div></div>et al. </span><div class="article-title">The OBO foundry: coordinated evolution of ontologies to support biomedical data integration</div>, <div class="source ">Nat. Biotechnol.</div>, <div class="year">2007</div>, vol. <div class="volume">25</div> (pg. <div class="fpage">1251</div>-<div class="lpage">1255</div>)<div class="citation-links"></div><div class="citation-links"><p class="citation-links-compatibility"><span class="google-scholar-ref-link"><a class="openInAnotherWindow" href="https://scholar.google.com/scholar_lookup?title=The%20OBO%20foundry%3A%20coordinated%20evolution%20of%20ontologies%20to%20support%20biomedical%20data%20integration&author=S.%20Barry&publication_year=2007&journal=Nat.%20Biotechnol.&volume=25&pages=1251-1255" target="_blank">Google Scholar</a></span></p><div class="pub-id"><a href="http://www.ncbi.nlm.nih.gov/pubmed/17989687" class="link link-pub-id openInAnotherWindow" target="_blank">PubMed</a></div><div class="xslopenurl empty-target"><span class="js-inst-open-url-holders-nodoi"><a class="js-open-url-link" data-href-template="{targetURL}?sid=oup:orr&genre=article&atitle=The+OBO+foundry%3a+coordinated+evolution+of+ontologies+to+support+biomedical+data+integration&aulast=Barry&title=Nat.+Biotechnol.&date=2007&spage=1251&epage=1255&volume=25" href="javascript:;"><span class="screenreader-text">OpenURL Placeholder Text</span></a></span></div><p class="citation-links-compatibility"><span class="worldcat-reference-ref-link js-worldcat-preview-ref-link" style="display:none"><a class="openInAnotherWindow" href="https://www.worldcat.org/search?q=ti:The%20OBO%20foundry%3A%20coordinated%20evolution%20of%20ontologies%20to%20support%20biomedical%20data%20integration&qt=advanced&dblist=638" target="_blank">WorldCat</a></span></p> </div></div></div></div></div><div content-id="B4" class="js-splitview-ref-item" data-legacy-id="B4"><div class="refLink-parent"><span class="refLink"><a name="jumplink-B4" href="javascript:;" aria-label="jumplink-B4" data-id=""></a></span></div><div class="ref false"><div id="ref-auto-B4" class="ref-content " data-id="B4"><div class="citation element-citation"><span class="person-group"><div class="name"><div class="surname">Cline</div> <div class="given-names">M.S.</div></div>et al. </span><div class="article-title">Integration of biological networks and gene expression data using Cytoscape</div>, <div class="source ">Nat. Protocol.</div>, <div class="year">2007</div>, vol. <div class="volume">2</div> (pg. <div class="fpage">2366</div>-<div class="lpage">2382</div>)<div class="citation-links"></div><div class="citation-links"><p class="citation-links-compatibility"><span class="google-scholar-ref-link"><a class="openInAnotherWindow" href="https://scholar.google.com/scholar_lookup?title=Integration%20of%20biological%20networks%20and%20gene%20expression%20data%20using%20Cytoscape&author=M.S.%20Cline&publication_year=2007&journal=Nat.%20Protocol.&volume=2&pages=2366-2382" target="_blank">Google Scholar</a></span></p><div class="crossref-doi js-ref-link"><a class="openInAnotherWindow" href="http://dx.doi.org/10.1038/nprot.2007.324" target="_blank">Crossref</a></div><div class="adsDoiReference hide"><a class="openInAnotherWindow" href="http://adsabs.harvard.edu/cgi-bin/basic_connect?qsearch=10.1038%2Fnprot.2007.324" target="_blank">Search ADS</a></div><div class="xslopenurl empty-target"><span class="inst-open-url-holders" data-targetId="10.1038%2Fnprot.2007.324"> </span></div><p class="citation-links-compatibility"><span class="worldcat-reference-ref-link js-worldcat-preview-ref-link" style="display:none"><a class="openInAnotherWindow" href="https://www.worldcat.org/search?q=ti:Integration%20of%20biological%20networks%20and%20gene%20expression%20data%20using%20Cytoscape&qt=advanced&dblist=638" target="_blank">WorldCat</a></span></p> </div></div></div></div></div><div content-id="B5" class="js-splitview-ref-item" data-legacy-id="B5"><div class="refLink-parent"><span class="refLink"><a name="jumplink-B5" href="javascript:;" aria-label="jumplink-B5" data-id=""></a></span></div><div class="ref false"><div id="ref-auto-B5" class="ref-content " data-id="B5"><div class="citation element-citation"><span class="person-group"><div class="name"><div class="surname">Cote</div> <div class="given-names">R.G.</div></div>et al. </span><div class="article-title">The ontology lookup service: more data and better tools for controlled vocabulary queries</div>, <div class="source ">Nucleic Acids Res.</div>, <div class="year">2008</div>, vol. <div class="volume">36</div> <div class="issue">Suppl. 2</div>(pg. <div class="fpage">W372</div>-<div class="lpage">W376</div>)<div class="citation-links"></div><div class="citation-links"><p class="citation-links-compatibility"><span class="google-scholar-ref-link"><a class="openInAnotherWindow" href="https://scholar.google.com/scholar_lookup?title=The%20ontology%20lookup%20service%3A%20more%20data%20and%20better%20tools%20for%20controlled%20vocabulary%20queries&author=R.G.%20Cote&publication_year=2008&journal=Nucleic%20Acids%20Res.&volume=36&pages=W372-W376" target="_blank">Google Scholar</a></span></p><div class="crossref-doi js-ref-link"><a class="openInAnotherWindow" href="http://dx.doi.org/10.1093/nar/gkn252" target="_blank">Crossref</a></div><div class="adsDoiReference hide"><a class="openInAnotherWindow" href="http://adsabs.harvard.edu/cgi-bin/basic_connect?qsearch=10.1093%2Fnar%2Fgkn252" target="_blank">Search ADS</a></div><div class="xslopenurl empty-target"><span class="inst-open-url-holders" data-targetId="10.1093%2Fnar%2Fgkn252"> </span></div><div class="pub-id"><a href="http://www.ncbi.nlm.nih.gov/pubmed/18467421" class="link link-pub-id openInAnotherWindow" target="_blank">PubMed</a></div><p class="citation-links-compatibility"><span class="worldcat-reference-ref-link js-worldcat-preview-ref-link" style="display:none"><a class="openInAnotherWindow" href="https://www.worldcat.org/search?q=ti:The%20ontology%20lookup%20service%3A%20more%20data%20and%20better%20tools%20for%20controlled%20vocabulary%20queries&qt=advanced&dblist=638" target="_blank">WorldCat</a></span></p> </div></div></div></div></div><div content-id="B6" class="js-splitview-ref-item" data-legacy-id="B6"><div class="refLink-parent"><span class="refLink"><a name="jumplink-B6" href="javascript:;" aria-label="jumplink-B6" data-id=""></a></span></div><div class="ref false"><div id="ref-auto-B6" class="ref-content " data-id="B6"><div class="citation element-citation"><span class="person-group"><div class="name"><div class="surname">Gentleman</div> <div class="given-names">R.</div></div></span>, <div class="source ">R Programming for Bioinformatics.</div>, <div class="year">2008</div><div class="publisher-name">Chapman & Hall\CRC</div><div class="citation-links"></div><div class="citation-links"><p class="citation-links-compatibility"><span class="google-scholar-ref-link"><a class="openInAnotherWindow" href="https://scholar.google.com/scholar_lookup?title=R%20Programming%20for%20Bioinformatics.&author=R.%20Gentleman&publication_year=2008&book=R%20Programming%20for%20Bioinformatics." target="_blank">Google Scholar</a></span></p><div class="crossref-doi js-ref-link"><a class="openInAnotherWindow" href="http://dx.doi.org/10.1201/9781420063684" target="_blank">Crossref</a></div><div class="adsDoiReference hide"><a class="openInAnotherWindow" href="http://adsabs.harvard.edu/cgi-bin/basic_connect?qsearch=10.1201%2F9781420063684" target="_blank">Search ADS</a></div><div class="xslopenurl empty-target"><span class="inst-open-url-holders" data-targetId="10.1201%2F9781420063684"> </span></div><p class="citation-links-compatibility"><span class="google-preview-ref-link js-google-preview-ref-link" style="display:none"><a class="openInAnotherWindow" href="https://www.google.com/search?q=R%20Programming%20for%20Bioinformatics.&btnG=Search+Books&tbm=bks&tbo=1" target="_blank">Google Preview</a></span></p><p class="citation-links-compatibility"><span class="worldcat-reference-ref-link js-worldcat-preview-ref-link" style="display:none"><a class="openInAnotherWindow" href="https://www.worldcat.org/search?q=ti:R%20Programming%20for%20Bioinformatics.&qt=advanced&dblist=638" target="_blank">WorldCat</a></span></p><div class="copac-reference-ref-link js-copac-preview-ref-link" style="display:none" data-pubtype="book"><span class="inst-copac"><a class="openInAnotherWindow" target="_blank" href="http://copac.ac.uk/search?ti=R%20Programming%20for%20Bioinformatics.">COPAC</a></span></div> </div></div></div></div></div><div content-id="B7" class="js-splitview-ref-item" data-legacy-id="B7"><div class="refLink-parent"><span class="refLink"><a name="jumplink-B7" href="javascript:;" aria-label="jumplink-B7" data-id=""></a></span></div><div class="ref false"><div id="ref-auto-B7" class="ref-content " data-id="B7"><div class="citation element-citation"><span class="person-group"><div class="name"><div class="surname">Horridge</div> <div class="given-names">M.</div></div> <div class="name"><div class="surname">Bechhofer</div> <div class="given-names">S.</div></div></span><div class="article-title">The OWL API: a Java API for working with OWL 2 ontologies</div>, <div class="source ">OWLED 2009, 6th OWL Experienced and Directions Workshop.</div>, <div class="year">2009</div><div class="publisher-loc">Virginia</div><div class="publisher-name">Chantilly</div><div class="citation-links"><p class="citation-links-compatibility"><span class="google-scholar-ref-link"><a class="openInAnotherWindow" href="https://scholar.google.com/scholar_lookup?title=OWLED%202009%2C%206th%20OWL%20Experienced%20and%20Directions%20Workshop.&author=M.%20Horridge&author=S.%20Bechhofer&publication_year=2009&book=OWLED%202009%2C%206th%20OWL%20Experienced%20and%20Directions%20Workshop." target="_blank">Google Scholar</a></span></p><p class="citation-links-compatibility"><span class="google-preview-ref-link js-google-preview-ref-link" style="display:none"><a class="openInAnotherWindow" href="https://www.google.com/search?q=OWLED%202009%2C%206th%20OWL%20Experienced%20and%20Directions%20Workshop.&btnG=Search+Books&tbm=bks&tbo=1" target="_blank">Google Preview</a></span></p><div class="xslopenurl empty-target"><span class="js-inst-open-url-holders-nodoi"><a class="js-open-url-link" data-href-template="{targetURL}?sid=oup:orr&genre=book&title=OWLED+2009%2c+6th+OWL+Experienced+and+Directions+Workshop.&aulast=Horridge&date=2009" href="javascript:;"><span class="screenreader-text">OpenURL Placeholder Text</span></a></span></div><p class="citation-links-compatibility"><span class="worldcat-reference-ref-link js-worldcat-preview-ref-link" style="display:none"><a class="openInAnotherWindow" href="https://www.worldcat.org/search?q=ti:OWLED%202009%2C%206th%20OWL%20Experienced%20and%20Directions%20Workshop.&qt=advanced&dblist=638" target="_blank">WorldCat</a></span></p><div class="copac-reference-ref-link js-copac-preview-ref-link" style="display:none" data-pubtype="book"><span class="inst-copac"><a class="openInAnotherWindow" target="_blank" href="http://copac.ac.uk/search?ti=OWLED%202009%2C%206th%20OWL%20Experienced%20and%20Directions%20Workshop.">COPAC</a></span></div> </div></div></div></div></div><div content-id="B8" class="js-splitview-ref-item" data-legacy-id="B8"><div class="refLink-parent"><span class="refLink"><a name="jumplink-B8" href="javascript:;" aria-label="jumplink-B8" data-id=""></a></span></div><div class="ref false"><div id="ref-auto-B8" class="ref-content " data-id="B8"><div class="citation element-citation"><span class="person-group"><div class="name"><div class="surname">Lacy</div> <div class="given-names">L.W.</div></div></span>, <div class="source ">OWL: representing Information Using the Web Ontology Language.</div>, <div class="year">2005</div><div class="publisher-loc">Victoria, BC</div><div class="publisher-name">Trafford Publishing</div><div class="citation-links"><p class="citation-links-compatibility"><span class="google-scholar-ref-link"><a class="openInAnotherWindow" href="https://scholar.google.com/scholar_lookup?title=OWL%3A%20representing%20Information%20Using%20the%20Web%20Ontology%20Language.&author=L.W.%20Lacy&publication_year=2005&book=OWL%3A%20representing%20Information%20Using%20the%20Web%20Ontology%20Language." target="_blank">Google Scholar</a></span></p><p class="citation-links-compatibility"><span class="google-preview-ref-link js-google-preview-ref-link" style="display:none"><a class="openInAnotherWindow" href="https://www.google.com/search?q=OWL%3A%20representing%20Information%20Using%20the%20Web%20Ontology%20Language.&btnG=Search+Books&tbm=bks&tbo=1" target="_blank">Google Preview</a></span></p><div class="xslopenurl empty-target"><span class="js-inst-open-url-holders-nodoi"><a class="js-open-url-link" data-href-template="{targetURL}?sid=oup:orr&genre=book&title=OWL%3a+representing+Information+Using+the+Web+Ontology+Language.&aulast=Lacy&date=2005" href="javascript:;"><span class="screenreader-text">OpenURL Placeholder Text</span></a></span></div><p class="citation-links-compatibility"><span class="worldcat-reference-ref-link js-worldcat-preview-ref-link" style="display:none"><a class="openInAnotherWindow" href="https://www.worldcat.org/search?q=ti:OWL%3A%20representing%20Information%20Using%20the%20Web%20Ontology%20Language.&qt=advanced&dblist=638" target="_blank">WorldCat</a></span></p><div class="copac-reference-ref-link js-copac-preview-ref-link" style="display:none" data-pubtype="book"><span class="inst-copac"><a class="openInAnotherWindow" target="_blank" href="http://copac.ac.uk/search?ti=OWL%3A%20representing%20Information%20Using%20the%20Web%20Ontology%20Language.">COPAC</a></span></div> </div></div></div></div></div><div content-id="B9" class="js-splitview-ref-item" data-legacy-id="B9"><div class="refLink-parent"><span class="refLink"><a name="jumplink-B9" href="javascript:;" aria-label="jumplink-B9" data-id=""></a></span></div><div class="ref false"><div id="ref-auto-B9" class="ref-content " data-id="B9"><div class="citation element-citation"><span class="person-group"><div class="name"><div class="surname">Motik</div> <div class="given-names">B.</div></div>et al. </span><div class="article-title">Hypertableau reasoning for description logics</div>, <div class="source ">J. Art. Intell. 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(pg. <div class="fpage">W170</div>-<div class="lpage">W173</div>)<div class="citation-links"></div><div class="citation-links"><p class="citation-links-compatibility"><span class="google-scholar-ref-link"><a class="openInAnotherWindow" href="https://scholar.google.com/scholar_lookup?title=BioPortal%3A%20ontologies%20and%20integrated%20data%20resources%20at%20the%20click%20of%20a%20mouse&author=N.F.%20Noy&publication_year=2009&journal=Nucleic%20Acids%20Res.&volume=37&pages=W170-W173" target="_blank">Google Scholar</a></span></p><div class="crossref-doi js-ref-link"><a class="openInAnotherWindow" href="http://dx.doi.org/10.1093/nar/gkp440" target="_blank">Crossref</a></div><div class="adsDoiReference hide"><a class="openInAnotherWindow" href="http://adsabs.harvard.edu/cgi-bin/basic_connect?qsearch=10.1093%2Fnar%2Fgkp440" target="_blank">Search ADS</a></div><div class="xslopenurl empty-target"><span class="inst-open-url-holders" data-targetId="10.1093%2Fnar%2Fgkp440"> </span></div><div 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ontoCAT: an R package for ontology traversal and search | Bioinformatics | Oxford Academic