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Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies. </p> <p> <strong>OntoCAT</strong> exists in many flavours including a stand-alone database and browser, REST service, Google App application and <a class="wiki" href="/wiki/r">ontoCAT R package</a> to work with ontologies in R environment. See <a class="wiki" href="/wiki/OntocatDownload#AlternativeOntoCATversions">download page</a> for all the options. </p> <p> The current repertoire of supported ontology resources can easily be extended for other resources. Such services would only need to implement the <a class="missing source">OntologyService</a> interface to immediately become aligned with pre-existing resources and allow for their seamless interchangeability. </p> <p> Releases are often and <a class="ext-link" href="http://www.molgenis.org:8080/hudson/job/ontocat/"><span class="icon"></span>tested nightly</a>, so that you never have to worry about the updates in the underlying resources. </p> <p> <strong>OntoCAT</strong> is open source and available under the <a class="ext-link" href="http://www.gnu.org/licenses/lgpl.html"><span class="icon"></span>LGPLv3 license</a>. </p> <h1 id="Howtociteus">How to cite us</h1> <p> <strong>OntoCAT - simple ontology search and integration in Java, R and REST/JavaScript</strong> <em>Tomasz Adamusiak, Tony Burdett, Natalja Kurbatova, K Joeri van der Velde, Niran Abeygunawardena, Despoina Antonakaki, Misha Kapushesky, Helen Parkinson and Morris A. Swertz</em> BMC Bioinformatics 2011, 12:218 <a style="padding:0; border:none" href="http://www.biomedcentral.com/1471-2105/12/218/"><img src="http://www.biomedcentral.com/bmcimages/browse/highlyaccessed.gif" alt="http://www.biomedcentral.com/bmcimages/browse/highlyaccessed.gif" crossorigin="anonymous" title="http://www.biomedcentral.com/bmcimages/browse/highlyaccessed.gif" /></a> <a style="padding:0; border:none" href="http://www.biomedcentral.com/1471-2105/12/218/"><img src="http://www.biomedcentral.com/bmcimages/browse/OA.gif" alt="http://www.biomedcentral.com/bmcimages/browse/OA.gif" crossorigin="anonymous" title="http://www.biomedcentral.com/bmcimages/browse/OA.gif" /></a> <br /> <a class="ext-link" href="http://www.biomedcentral.com/1471-2105/12/218/"><span class="icon"></span>Article</a> | <a class="missing attachment">BibTeX</a> </p> <p> <strong>ontoCAT: an R package for ontology traversal and search</strong> <em>Kurbatova N, Adamusiak T, Kurnosov P, Swertz MA, Kapushesky M.</em> Bioinformatics. 2011 Jun 22.<br /> <a class="ext-link" href="http://bioinformatics.oxfordjournals.org/content/early/2011/06/22/bioinformatics.btr375.abstract"><span class="icon"></span>Abstract</a> </p> <h1 id="Posterstalks">Posters & talks</h1> <p> [Semantic Web] OntoCAT - an integrated programming toolkit for common ontology application tasks, The 12th Annual Bioinformatics Open Source Conference (BOSC 2011), co-located with ISMB/ECCB 2011, Vienna, Austria. Slides available from <a class="ext-link" href="http://slidesha.re/mXlCVl"><span class="icon"></span>http://slidesha.re/mXlCVl</a> </p> <p> Adamusiak Tomasz, Burdett Tony, van der Velde K Joeri, Abeygunawardena Niran, Antonakaki Despoina, Parkinson Helen, and Swertz Morris. OntoCAT – a simpler way to access ontology resources. Available from Nature Precedings <<a class="ext-link" href="http://dx.doi.org/10.1038/npre.2010.4666.1"><span class="icon"></span>http://dx.doi.org/10.1038/npre.2010.4666.1</a>> (2010) </p> <h1 id="Contact">Contact</h1> <p> Support is provided by the <a class="ext-link" href="https://lists.sourceforge.net/lists/listinfo/ontocat-users"><span class="icon"></span>ontocat-users</a> mailing list. Past questions are available in the <a class="ext-link" href="http://sourceforge.net/mailarchive/forum.php?forum_name=ontocat-users"><span class="icon"></span>list archive</a>. </p> <h2 id="Corecontributors">Core contributors</h2> <p> Tomasz Adamusiak <tomasz@…> </p> <p> Morris Swertz <m.a.swertz@…> </p> <p> Natalja Kurbatova <natalja@…> </p> <h1 id="Relatedprojects">Related projects</h1> <ul><li><strong><a class="ext-link" href="http://www.ebi.ac.uk/efo"><span class="icon"></span>Experimental Factor Ontology</a></strong> </li><li><strong><a class="ext-link" href="http://dbnp.org/"><span class="icon"></span>Nutritional Phenotype Database (DbNP)</a></strong> </li></ul><h1 id="Acknowledgements">Acknowledgements</h1> <p> OntoCAT has been developed in the framework of the European Commission's Seventh Framework Programme <a class="ext-link" href="http://www.gen2phen.org"><span class="icon"></span>GEN2PHEN project</a> (grant number 226073), which aims to unify human and model organism genetic variation databases towards increasingly holistic views into Genotype-To-Phenotype (G2P) data. The GEN2PHEN Consortium members have been selected from a talented pool of European research groups and companies that are interested in the G2P database challenge. Additionally, a few non-EU participants have been included to bring extra capabilities to the initiative. </p> <p> This work was also supported by the FP7 Programmes: SLING (grant number 226073), and SYBARIS (grant number 242220), the European Molecular Biology Laboratory, the Netherlands Organisation for Scientific Research (NWO/Rubicon grant number 825.09.008), and the Netherlands Bioinformatics Centre (BioAssist/Biobanking platform and BioRange grant SP1.2.3). </p> <p> OntoCAT's development is a joint effort between the <a class="ext-link" href="http://www.ebi.ac.uk/fg/"><span class="icon"></span>Functional Genomics Group</a> at the European Informatics Institute, UK and <a class="ext-link" href="http://wiki.gcc.rug.nl/wiki/GccStart"><span class="icon"></span>the Genomics Coordination Center</a>, University Medical Center Groningen, the Netherlands. </p> <p> Special thanks go to NCBO BioPortal and EBI OLS support teams for all the comprehensive help they provide. </p> <p> OntoCAT logo courtesy of Eamonn Maguire. </p> </div> <div class="trac-modifiedby"> <span><a href="/wiki/OntocatStart?action=diff&version=3" title="Version 3 by Morris Swertz">Last modified</a> <a class="timeline" href="/timeline?from=2021-04-30T09%3A36%3A37%2B02%3A00&precision=second" title="See timeline at 2021-04-30T09:36:37+02:00">4 years ago</a></span> <span class="trac-print">Last modified on 2021-04-30T09:36:37+02:00</span> </div> </div> </div> <div id="altlinks"> <h3>Download in other formats:</h3> <ul> <li class="last first"> <a rel="nofollow" href="/wiki/OntocatStart?format=txt">Plain Text</a> </li> </ul> </div> </div> <div id="footer" lang="en" xml:lang="en"><hr /> <a id="tracpowered" href="https://trac.edgewall.org/"><img src="/chrome/common/trac_logo_mini.png" height="30" width="107" alt="Trac Powered" /></a> <p class="left">Powered by <a href="/about"><strong>Trac 1.2.6</strong></a><br /> By <a href="http://www.edgewall.org/">Edgewall Software</a>.</p> <p class="right">Visit the Trac open source project at<br /><a href="https://trac.edgewall.org/">https://trac.edgewall.org/</a></p> </div> </body> </html>