You can find a summary of the new functionality, enhancements and fixes below.
As usual, we would like to thank all of our users who reported issues and suggested new functionality. In particular, we would like to thank members of the OBO community for their input with regards to some of the new features mentioned below.
This release provides new functionality, enhancements to existing functionality and also fixes various bugs.
Added a preference panel for specifying the logged in user. This can be used by plugins and is also used when auto-creation of metadata is enabled.
It is now possible to automatically attach meta-data to freshly created classes (#283). Thanks go to @cmungall for
suggesting this and for input from the OBO community for contribution of ideas (in particular @tberardini, @mellybelly, @mcourtot, @dosumis).
Images that are pointed to by annotation values are now displayed inline as thumbnails (#315)
Made the search engine that Protege uses pluggable (a Lucene search plugin is on the way) (#284)
Asserted and inferred hierarchies are now combined into single views. They can be switched using the drop down box, or by pressing "a" for asserted or "i" for inferred when the associated view has the focus. (#145)
Cleaned up the metrics view by removing unnecessary clutter
Copying errors from the log view to the clipboard now includes stack traces (#297)
Added a button for clearing the log in the log view (#296)
The error icon is now cleared after the log view is closed (#305)
Cleaned up and refined the user interface and reduced clutter where possible
Moved the log file location to the user home directory (#299)
Fixed a problem where Protege did not detect when loaded source files had changed externally and offer to reload them (#300)
Fixed a problem with syntax checking in the general class axioms view (#302)
The object property hierarchy now displays sub-properties correctly (#306)
Added a log message to describe when plugin update files cannot be parsed
Removed formatting markers that showed up in console logs on Windows (#303)
Added a missing flag to the Windows run.bat file that ensures array index out of bound exceptions do not occur (#307 and #226)
Fixed a problem with adding data ranges to properties (#308)
Fixed a problem that caused icons on tabs to be painted incorrectly (#309)
Well known IRIs that have well known prefixes are now rendered as prefix names regardless of the selected renderer (#310)
The auto-complete would not match annotation properties (#311)
Fixed a problem where "Optional" would appear in ontology IRIs rendered in the user interface (#313)
Fixed a problem where imported ontologies were loaded using the incorrect OWL API method. This could cause import loading to raise errors when adding imports (#314)
Changed the accelerator key for copying tab indented text from hierarchies because it clashed with the copy accelerator key (#316)
Made it possible to copy class names from the class hierarchy (#222)
Adjusted run scripts so that they work better with symbolic links (#318) (thanks go to @ShahimEssaid for
Fixed a problem where the explanation dialog would raise an error if there were no explanation plugins installed (#319)
Fixed a problem with drag being enabled when it was disabled in the UI preferences (#322)
Fixed a problem where an inconsistent ontology exception would leak out from the inferred object property hierarchy (#328)
Fixed a problem where "Render by Prefixed Annotation property would display two prefixes (#327)