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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

Documentation and code available from http://code.google.com/p/owltools/