How to convert an OBO ontology to OWL

How to convert an OBO ontology to OWL, e.g. the Sequence Ontology

These instructions for Mac OS X, using the GO perl tools.

Download
 * http://search.cpan.org/CPAN/authors/id/C/CM/CMUNGALL/Data-Stag-0.09.tar.gz
 * http://search.cpan.org/CPAN/authors/id/C/CM/CMUNGALL/go-perl-0.04.tar.gz

Latest versions of the packages can be found in http://search.cpan.org/~cmungall/

Install them as follows (assumes you are in the download directory)

tar xvfz Data-Stag-0.09.tar.gz cd Data-Stag-0.09 perl Makefile.PL sudo make install cd .. tar xvfz go-perl-0.04.tar.gz cd go-perl-0.04 perl Makefile.PL sudo make install

There will be some complaints about packages to install for various functions. For the conversion I found that I only needed the ones listed above, however it is possible that I had installed some things it depends on earlier.

Now, in the directory with the obo file, e.g. so.obo  should do the conversion. (you might have to tell your shell to, so it picks up the scripts which were installed in /usr/bin)

The conversion has the class names being the obo identifiers, which makes it hard to read. You can have them displayed in the Protege UI by following these instructions from Matthew Horridge:

''You need to make owl:Class visible (go to the OWL preferences and select the visibility tab). Next go to the forms tab and make sure owl:Class is selected. Change the "Display Slot" to rdfs:label using the drop down box at the top of the form''

Alan Ruttenberg