OWLTools

OWLTools (aka OWL2LS - OWL2 Life Sciences) is convenience java API on top of the OWL API. It provides

• convenience methods for OBO-like properties such as synonyms, textual definitions, obsoletion, replaced_by
• simple graph-like operations over ontologies
• visualization using the QuickGO graphs libraries

Java Docs

The javadocs can be browsed here:

• http://berkeleybop.org/owltools

Source

The source is CURRENTLY available on sourceforge, but is moving:

• Browse OWLTools

 svn co  https://geneontology.svn.sourceforge.net/svnroot/geneontology/OWLTools

New destination:

• http://code.google.com/p/owltools/

Dependencies

All required jars are included in the distribution. Notable dependencies are

• the OWL API (http://owlapi.sourceforge.net).
  • in fact much of the owltools functionality is in providing a simple layer on the OWLAPI
• org.oboformat (http://code.google.com/p/oboformat/).
  • this is only used if you are parsing owl ontologies from obo format. there are significant improvements over the obo parser that is part of the owlapi