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

  • 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
  • Semantic similarity of OWL individuals and classes (OwlSim)
  • Powerful command line interface
  • JS/Rhino REPL

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


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