Hello, I am working on a project and I need to use the cell line ontology(CLO). I tried accessing CLO using protege but faced problems accessing it, I wrote an email to the creator of the cell line ontology to figure out the problem but didn't get any response. I was wondering if there is a way to parse the OWL file using Perl, I tried to convert the OWL to OBO using Perl OWL to OBO converter but couldn't get all the data. Is there a way to parse the OWL based ontology.
Protege, as you mentioned, is indeed the standard way to parse OWL files. Perhaps you should tell us the problem you ran into while using it or post it to their mailing list.
Of course, there is also the possibility of going on even lower levels and using and XML library or direct text parsing. However, I would (1) explain what problem you have using Protege and (2) if that doesn't work query it with using SPARQL.