OWLTools (aka OWL2LS - OWL2 Life Sciences) is convenience java API on top of the OWL API. It provides many features, including:
Oort is also distributed as part of OWLTools
The javadocs can be browsed here:
For detailed documentation, start with the OWLTools Introduction.
OWLTools relies heavily on the Manchester OWLAPI, familiarity with this helps - see the OWLAPI tutorial
The list is mirrored as a googlegroup. You can use either of the two: