CODEWITHSUNDEEP
perlxml-parsingowlontology
Jack
Jack

Reputation: 371

Convert OWL Ontology to OBO

I need to convert a OWL ontology to OBO.

I've tried this tool https://github.com/ontodev/robot/ but the output format isn't correct at all, just some parts.

Also OBO-EDIT2 and Protegé but the weren't able to do a conversion.

Lastly I've tried this Perl module http://search.cpan.org/~easr/ however it gives this error

Undefined subroutine &XML::Parser called at /usr/local/share/perl/5.14.2/OBO/Parser/OWLParser.pm line 146.

And trying to install XML::Parser always ends with an error.

Could anyone help me to convert the Ontology?

Upvotes: 7

Views: 1266

Answers (2)

Ignazio
Ignazio

Reputation: 10659

If you're using OWL API, OBO is one of the supported output formats. It is sufficient to pass an OBODocumentFormat to the saveOntology() method.

Upvotes: 1

user52889
user52889

Reputation: 1501

Have you tried https://github.com/owlcollab/owltools/?

And trying to install XML::Parser always ends with an error.

What commands are you running to install XML::Parser? What is that error? Can you install other perl modules ok with the same commands? What about ones which require make?

Upvotes: 1

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