| | 1 | [[BlogList(recent=5, max_size=250, format=float, heading=News)]] |
| | 2 | |
| | 3 | = About = |
| | 4 | '''OntoCAT''' provides high level abstraction for interacting with ontology resources including local ontology files in standard OWL and |
| | 5 | 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. |
| | 6 | |
| | 7 | '''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. |
| | 8 | |
| | 9 | 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. |
| | 10 | |
| | 11 | 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. |
| | 12 | |
| | 13 | '''OntoCAT''' is open source and available under the [http://www.gnu.org/licenses/lgpl.html LGPLv3 license]. |
| | 14 | |
| | 15 | = How to cite us = |
| | 16 | '''OntoCAT - simple ontology search and integration in Java, R and REST/JavaScript''' |
| | 17 | ''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 |
| | 18 | [[Image(http://www.biomedcentral.com/bmcimages/browse/highlyaccessed.gif, link=http://www.biomedcentral.com/1471-2105/12/218/)]] |
| | 19 | [[Image(http://www.biomedcentral.com/bmcimages/browse/OA.gif, link=http://www.biomedcentral.com/1471-2105/12/218/)]] |
| | 20 | [[br]] |
| | 21 | [http://www.biomedcentral.com/1471-2105/12/218/ Article] | [attachment:ontocat.bib BibTeX] |
| | 22 | |
| | 23 | '''ontoCAT: an R package for ontology traversal and search''' |
| | 24 | ''Kurbatova N, Adamusiak T, Kurnosov P, Swertz MA, Kapushesky M.'' Bioinformatics. 2011 Jun 22.[[br]] |
| | 25 | [http://bioinformatics.oxfordjournals.org/content/early/2011/06/22/bioinformatics.btr375.abstract Abstract] |
| | 26 | |
| | 27 | = Posters & talks = |
| | 28 | [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 |
| | 29 | |
| | 30 | 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) |
| | 31 | |
| | 32 | = Contact = |
| | 33 | 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]. |
| | 34 | == Core contributors == |
| | 35 | Tomasz Adamusiak <tomasz@mcw.edu> |
| | 36 | |
| | 37 | Morris Swertz <m.a.swertz@rug.nl> |
| | 38 | |
| | 39 | Natalja Kurbatova <natalja@ebi.ac.uk> |
| | 40 | = Related projects = |
| | 41 | * '''[http://www.ebi.ac.uk/efo Experimental Factor Ontology]''' |
| | 42 | * '''[http://dbnp.org/ Nutritional Phenotype Database (DbNP)]''' |
| | 43 | |
| | 44 | = Acknowledgements = |
| | 45 | |
| | 46 | 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. |
| | 47 | |
| | 48 | 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). |
| | 49 | |
| | 50 | 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. |
| | 51 | |
| | 52 | Special thanks go to NCBO !BioPortal and EBI OLS support teams for all the comprehensive help they provide. |
| | 53 | |
| | 54 | OntoCAT logo courtesy of Eamonn Maguire. |
