Protégé 5.2.0

This release contains various enhancements and fixes. Please note that if you are running MacOS Sierra then you may have to take some steps to enable the native Protege application to run.

Improvements & Enhancements

Context Sensitive Help

• We have added context sensitive help to many of the views in Protégé. If help is available for a view then that help can be shown by pressing the "question mark" button in the view header. Help documentation ultimately points to here.

  

  (protegeproject/protege#587)

• We have also added help documentation for the class expression syntax that is used in Protege. The help documentation can be displayed via the help button on the class expression editor dialog. Documentation can be found here.

  (protegeproject/protege#592 and protegeproject/protege#593)

Entities Tab Improvements

• PubMed Ids in annotations that contain white space are now parsed and displayed as links to PubMed (protegeproject/protege#615)
• Anonymous individuals that are auto-created for use in annotation values are no longer prefixed with the ontology Id
• Entity names in lists are no longer quoted with single quotes in order to improve readability.

General User Interface Improvements

• Changed the title of "Capture View..." in the Window menu to "Capture view to clipboard..." (protegeproject/protege#570)
• Class creation buttons above the class hierarchy view are now disabled if the inferred class hierarchy is shown (protegeproject/protege#579)
• Improved the axiom annotations editing dialog so that it is correctly sized for axioms that have long renderings (protegeproject/protege#577 and protegeproject/protege#594)
• Added and updated help items on the help menu (protegeproject/protege#588)

Changes for Developers

• Updated to the OWL API version 4.2.8 (protegeproject/protege#616)
• Removed reference to internal sun package (protegeproject/protege#572). Thanks go to @mans0954.

Fixes

• Fixed a problem where the loading progress bar was not hidden on Linux (protegeproject/protege#574). Thanks go to @lks128 and @ykazakov for this fix.
• Window -> Capture View... could throw a Null Pointer Exception (protegeproject/protege#568)
• maven-artefact.jar was missing from the class path in the run.bat in the Windows distribution (protegeproject/protege#567)
• Delete Entity icons are now painted as disabled if the underlying component is disabled (protegeproject/protege#580)
• Fixed a problem that would cause a badly behaving listener error to be displayed if an explanation plugin was invoked (protegeproject/protege#410). Thanks go to @ykazakov for the fix.
• Release notes menu points to outdated release notes on the Protege wiki instead of GitHub (protegeproject/protege#591)
• Fixed a problem where "Save" and "Save As" could produce different orderings for ontologies saved in Turtle syntax, which could cause problems with using version control systems to store ontologies. (protegeproject/protege#609)
• Fixed a problem where the object property hierarchy would not be updated if the active ontology was changed (protegeproject/protege#606).
• Changed logging behaviour so that Protege only creates one log directory (protegeproject/protege#608).
• Fixed some problems with creating a class hierarchy from tab indented text if label rendering is used (protegeproject/protege#599)
• Improved the layout of the annotation property editor so that hierarchies are displayed in a better fashion (protegeproject/protege#544)
• Fixed a problem where the annotation editor window could be too large to be displayed on a screen (protegeproject/protege#581).