Re: [Obo-format] OBO to OWL Converters

[Erick A. <er...@ps...>]

Gary,

    besides the Protege plugin and the xsl file, there is also a Perl 
script (obo2owl.pl, bundled in a set of Perl modules for dealing with 
OBO ontologies) for doing the trick:

        http://search.cpan.org/~easr/onto-perl-0.31/

    which also implements the mapping described in the Google 
spreadsheet, we are trying to keep it as much as possible in sync with 
that mapping, it has been tested with our local ontologies and currently 
the owl generated files are used in our analysis. So in case you test 
the perl solution, please inform us about any problem. For using the 
obo2owl.pl script, just install the modules and type:
      
        perl obo2owl.pl my_ontology.obo > my_ontology.owl

    An article is being prepared for describing not only these three 
solutions (Dilvan's plugin, scripts from Chris and the Perl based one I 
mentioned) but also the details about the conversion,  more on this can 
be commented by Nigam and Chris.

Cheers,
Erick
P.S.[Off line]  
On the other hand, I have seen you guys at VPIN have developed also a 
OBO to OWL conversion solution in java 
(http://vpin.ncgr.org/PUBLIC_DOCS/developers_kits/OBOontologyConvert.zip) 
as well as other very interesting stuff for the plants domain which is 
actually our main business too. We have been also busy on building an 
infrastructure for knowledge elucidation in plants currently focused on 
the cell cycle process in arabidopsis (although we have also considered 
other model organisms and different processes such as apoptosis, too). 
Until now we have been exploiting some reasoning capabilities (with 
RACER mainly) by discovering inconsistent data (in our main sources) and 
querying interesting questions to the knowledge base. If you are 
interested, we can discuss further on this.

Gary Schiltz wrote:
> I looked at http://www.bioontology.org/wiki/index.php/OboInOwl:Main_Page 
> and would appreciate some clarification about the various approaches to 
> converting OBO to OWL. From reading the above page, I gather that there 
> are two pieces of software (the OBO Converter Tab for Protege and the 
> OboEdit OWL plugin) as well as an XML style sheet (oboxml_to_owl.xsl). 
> Here are some questions:
>
> 1. Does the OboEdit plugin use the same underlying code as the converter 
> tab for Protege? [by the way, trying to do a SVN checkout of the 
> converter tab code, i.e. 'svn co 
> http://smi-protege.stanford.edu/svn/obo-converter/trunk/', gives me a 
> "301 Moved" error; do I need to specify a username to get the code? 
> Although a pain, I used the "ViewCVS" interface to manually download 
> each file...]
>
> 2. I didn't find the source for the OboEdit plugin - is it open source, 
> and if so, would someone please send me a link?
>
> 3. The oboxml_to_owl.xsl style sheet requires an XML file as input. How 
> does one transform an OBO file to an XML file suitable for this style sheet?
>
> 4. Which of these converters most accurately implements the mapping 
> outlined on the Google spreadsheet referenced on the above page? The 
> style sheet seems to have been updated the most recently.
>
> Sorry for so many questions, and thanks in advance.
>
> ----
>
> Gary Schiltz
> Principal Software Engineer
> National Center for Genome Resources
> Santa Fe, New Mexico USA
>
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-- 
==================================================================
Erick Antezana                    http://www.cellcycleontology.org
PhD Student
Tel:32 (0)9 3313824                            Fax:32 (0)9 3313809
VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY, UGent
Technologiepark 927, 9052 Gent, BELGIUM
er...@ps...                         http://www.psb.ugent.be
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