Changes between Initial Version and Version 1 of OntocatStart


Ignore:
Timestamp:
2015-07-21T20:02:11+02:00 (9 years ago)
Author:
Morris Swertz
Comment:

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  • OntocatStart

    v1 v1  
     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
     5OBO 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
     9The 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
     11Releases 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
     30Adamusiak 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 =
     33Support 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 ==
     35Tomasz Adamusiak <tomasz@mcw.edu>
     36
     37Morris Swertz <m.a.swertz@rug.nl>
     38
     39Natalja 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
     46OntoCAT 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
     48This 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
     50OntoCAT'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
     52Special thanks go to NCBO !BioPortal and EBI OLS support teams for all the comprehensive help they provide.
     53
     54OntoCAT logo courtesy of Eamonn Maguire.