= About = '''OntoCAT''' provides high level abstraction for interacting with ontology resources including local ontology files in standard OWL and OBO formats (via '''[http://owlapi.sourceforge.net OWL API]''') and public ontology repositories: '''[http://www.ebi.ac.uk/ontology-lookup/ EBI Ontology Lookup Service (OLS)]''' and '''[http://bioportal.bioontology.org/ NCBO BioPortal]'''. 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. '''OntoCAT''' exists in many flavours including a stand-alone database and browser, REST service, Google App application and [wiki:r ontoCAT R package] to work with ontologies in R environment. See [wiki:OntocatDownload#AlternativeOntoCATversions download page] for all the options. The current repertoire of supported ontology resources can easily be extended for other resources. Such services would only need to implement the [source:trunk/ontoCAT/src/uk/ac/ebi/ontocat/OntologyService.java OntologyService] interface to immediately become aligned with pre-existing resources and allow for their seamless interchangeability. Releases are often and [http://www.molgenis.org:8080/hudson/job/ontocat/ tested nightly], so that you never have to worry about the updates in the underlying resources. '''OntoCAT''' is open source and available under the [http://www.gnu.org/licenses/lgpl.html LGPLv3 license]. = How to cite us = '''OntoCAT - simple ontology search and integration in Java, R and REST/JavaScript''' ''Tomasz Adamusiak, Tony Burdett, Natalja Kurbatova, K Joeri van der Velde, Niran Abeygunawardena, Despoina Antonakaki, Misha Kapushesky, Helen Parkinson and Morris A. Swertz'' BMC Bioinformatics 2011, 12:218 [[Image(http://www.biomedcentral.com/bmcimages/browse/highlyaccessed.gif, link=http://www.biomedcentral.com/1471-2105/12/218/)]] [[Image(http://www.biomedcentral.com/bmcimages/browse/OA.gif, link=http://www.biomedcentral.com/1471-2105/12/218/)]] [[br]] [http://www.biomedcentral.com/1471-2105/12/218/ Article] | [attachment:ontocat.bib BibTeX] '''ontoCAT: an R package for ontology traversal and search''' ''Kurbatova N, Adamusiak T, Kurnosov P, Swertz MA, Kapushesky M.'' Bioinformatics. 2011 Jun 22.[[br]] [http://bioinformatics.oxfordjournals.org/content/early/2011/06/22/bioinformatics.btr375.abstract Abstract] = Posters & talks = [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 http://slidesha.re/mXlCVl 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 <[http://dx.doi.org/10.1038/npre.2010.4666.1]> (2010) = Contact = Support is provided by the [https://lists.sourceforge.net/lists/listinfo/ontocat-users ontocat-users] mailing list. Past questions are available in the [http://sourceforge.net/mailarchive/forum.php?forum_name=ontocat-users list archive]. == Core contributors == Tomasz Adamusiak Morris Swertz Natalja Kurbatova = Related projects = * '''[http://www.ebi.ac.uk/efo Experimental Factor Ontology]''' * '''[http://dbnp.org/ Nutritional Phenotype Database (DbNP)]''' = Acknowledgements = OntoCAT has been developed in the framework of the European Commission's Seventh Framework Programme [http://www.gen2phen.org GEN2PHEN project] (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. 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). OntoCAT's development is a joint effort between the [http://www.ebi.ac.uk/fg/ Functional Genomics Group] at the European Informatics Institute, UK and [http://wiki.gcc.rug.nl/wiki/GccStart the Genomics Coordination Center], University Medical Center Groningen, the Netherlands. Special thanks go to NCBO !BioPortal and EBI OLS support teams for all the comprehensive help they provide. OntoCAT logo courtesy of Eamonn Maguire.