Transition to OWL 2013-2014

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Revision as of 16:36, 19 June 2013 by Cjm (talk | contribs) (Created page with " == Background == * In 2010 we drew up the Transition_to_OWL plan. The software group worked on migrating software to java/OWLAPI/OWLTools in 2010-2012 * In Jan 2012 we ...")
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Background

Successes

  • All software developed in GO now consumes the OWL as primary - obo is converted to OWL behind the scenes
  • We have many TermGenie templates, equivalence axioms are created prospectively rather than retrospectively
  • We have OWL reasoning as part of a continuous integration service - Jenkins
  • GO software group (Heiko) and collaborators have written plugins to help approximate OE behavior - Ontology_editor_plugins - thanks particularly to Jim Balhoff
  • Ontology editors are confident in using Protege to debug the ontology (e.g. explanation facility)
  • Ontology engineering has become more like software engineering
  • CL has switched to using OWL for the edit version, and GO editors participate in development

Weak points

  • Many OWL axioms are not visible or editable during normal ontology editing workflow in OBO-Edit
  • Entailments of those axioms are not visible
    • This necessitates cacheing entailments using is_inferred="true" axiom annotation
    • Additional complexity in workflow as cached entailments are re-checked, takes time to investigate

The weakpoints come down to lack of OWL support in OBO-Edit - particularly: working with >1 ontology, fast reasoning

The consensus is that Protege in its current state would lead to a loss of productivity in other areas

Plan

The ontology group will come up with recommendations before the Bar Harbor meeting (Oct 2013) and provide these to the software group.

We need to decide on where to spend resources

  • Adding more plugins to Protege to better approximate OBO-Edit? Can this be approximated with plugins or is the foundation flawed? Would more training help?
  • Adding