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OWLTools (aka OWL2LS - OWL2 Life Sciences) is convenience java API on top of the OWL API. It provides many including:
The javadocs can be browsed here: http://owlcollab.github.io/owltools/api/index.html
There is some legacy documentation here: http://wiki.geneontology.org/index.php/OWLTools
See also the overview of features