Protégé 5.1.0

This release contains various enhancements and fixes.

Improvements & Enhancements

Annotation Editing & Viewing

• The annotation value editor now indicates whether or not the entered value is in the lexical space of the selected datatype. For example, if the entered value was “Hello” but the datatype is specified as xsd:integer then an error message will be displayed. (protegeproject/protege#441)
• Annotation values that are anonymous individuals now have property assertions that the individual is a subject of displayed inline. (protegeproject/protege#443)
• Added usage of IRIs that are annotation values and correspond to entity IRIs to the kinds of usage displayed in the usage view. (protegeproject/protege#483)
• Annotation values that correspond to PubMed Ids are now shown as hyperlinks. When clicked a new browser window is opened and the corresponding Id is displayed on the PubMed Website. (protegeproject/protege#512)

• ISBNs in annotation values are now shown as hyperlinks. Clicking one of these links opens a new window displaying information about the ISBN. (protegeproject/protege#513)
• Wikipedia identifiers such as wikipedia:Cell that appear in annotation values are now shown as hyperlinks. Clicking such a link will open a browser window and display the relevant Wikipedia page. (protegeproject/protege#515)
• Improved the scrolling behaviour of annotation views when annotation values with large amounts of text are displayed. (protegeproject/protege#516)
• Changed the behaviour of the annotation value editor so that it focuses the actual editor when it is displayed. Previously, the annotation property list on the left hand side was focuses on open. (protegeproject/protege#537)

Entities Tab Improvements

• Changed the default layout of the Entities tab so that the left hand side is more spacious and so that it is clearer as to what is selected. Note that users who wish to see these changes should reset the layout of the Entities tab by selecting “Window” -> “Reset selected tab to default state”(protegeproject/protege#504)
• Improved the selection mechanism in the Protege User Interface. Switching a view that drives the selection (such as a tree) now causes the selection to be updated without having to reselect the entity in the tree. (protegeproject/protege#506 and protegeproject/protege#335)
• Changed the behaviour of the Entities tab so that the right hand side now indicates if there isn’t any entity selected. (protegeproject/protege#507)
• The right hand side entities tab nows displays the IRI for the selected entity (protegeproject/protege#525)

General User Interface Improvements

• Enhanced the About Box so that it displays more information including the current memory settings. (protegeproject/protege#508)
• Added support for scaling screen captures of views
• Updated the look and feel of the status bar so that it is more compact and neater. (protegeproject/protege#500)
• Enhanced the various trees in Protege so that vertical lines can be displayed for all look and feels. (protegeproject/protege#470)
• Changed the list of installed plugins on the Plugins preferences panel so that it is now ordered by plugin name. (protegeproject/protege#494)
• Improved the handling of plugin selection when multiple different versions of the same plugin are installed (protegeproject/protege#452)
• Removed verbose exception traces from the log view so that the view is more manageable. (protegeproject/protege#496)
• Improved the display of error messages during saving (protegeproject/protege#440)
• Changed the Individuals by Type view so that if a class in the view is selected when adding a new individual then the individual is typed with that class. (protegeproject/protege#177)
  (protegeproject/protege#538)
• Added functionality to make individuals of a specific class different from each other. (protegeproject/protege#523)
• Made it possible to copy the information displayed in the usage view (protegeproject/protege#466)
• Added help text to the New Entities Metadata preferences panel (protegeproject/protege#495)
• Improved the rendering of entity icons so that they are sharper on high resolution screens and when extra large font sizes are displayed.
• Made the enabling/disabling of menu items for class actions more uniform over the UI (protegeproject/protege#549)

Other Changes

• Renamed the “Close” item on the File menu to be “Close Window” so that its meaning is clearer. (protegeproject/protege#478)
• Changed the behaviour of applying ontology changes so that a minimised list of changes is applied. (protegeproject/protege#474)
• Improved the rendering in the usage view with regards to highlighting (protegeproject/protege#477)
• Added the ability to reset the History Manager. (protegeproject/protege#463)
• Added an error message that gets displayed if the user tries to edit the active ontology library but an ontology catalog is not present. (protegeproject/protege#497)
• Renamed “Edit Ontology Libraries” so that the meaning of this menu item is clearer. (protegeproject/protege#456)
• Updated the color of datatypes and made them uniform over all data type views (protegeproject/protege#503)

Changes for Developers

• EditorKit hooks are now initialised before the Workspace is initialised. (protegeproject/protege#529)
• Upgraded to the OWL API version 4.2.6 (protegeproject/protege#543)

Fixes

• Fixed a bug in the About Box so that it displays any qualifier information in the build number. (protegeproject/protege#446 and protegeproject/protege#447)
• Fixed a bug in font sizing in the metrics view (protegeproject/protege#449)
• Fixed a problem with the annotation of inferred axioms through the Protege UI (protegeproject/protege#462)
• Fixed a problem where the annotation value editor would not allow the selection of a language if the type was rdf:PlainLiteral (protegeproject/protege#464)
• Fixed a problem where the explain tools would cause a stack trace to be dumped to the console on exit. Thanks go to @ykazakov for this fix. (protegeproject/protege#410)
• Fixed a problem that could occur when recursively expanding class and property hierarchies. (protegeproject/protege#468)
• Fixed a problem where temporary folders were sometimes not deleted on exit (protegeproject/protege#461)
• Fixed a problem where auto-completion in the property expression editor would sometimes throw an error. (protegeproject/protege#460)
• Changed the “Edit ontology libraries…” file dialog so that it is a native file dialog. (protegeproject/protege#455)
• Fixed a problem where the UIUtil save dialog would not display the specified title. (protegeproject/protege#476)
• Fixed an issue where the General Class Axioms editor would throw errors on axioms other than SubClassOf axioms (protegeproject/protege#450)
• Addressed an issue where Protege would allow the active ontology to be programmatically removed. (protegeproject/protege#488 and protegeproject/protege#479)
• Fixed a problem where it was not possible to change the “creator” property in the New Entities Metadata preferences panel. (protegeproject/protege#486)
• Errors thrown in the initialisation of the object property hierarchy could ripple through to the UI - fixed. (protegeproject/protege#458)
• Fixed a bug where “Move axioms to ontology” did not work as expected. (protegeproject/protege#526)

Updates to Plugins

• Updated the DL Query Tab to version 4.0.1
• Updated Cellfie to 2.1.0. You can find detailed release notes here.