The contents of this page describe changes relative to Protégé 3.4.



Bug Fixes in Protégé-OWL

• Fixed a bug that caused an exception when saving an ontology to a non-existent directory.

Enhancements in Protégé-OWL

• A basic SWRL expression editor is now functional. Please be aware that only RDF/XML is recommended for saving ontologies containing rules.
• Temp files are now used when saving files. If exceptions are thrown, your original file will not be overwritten.
• Refactoring support for disjoints (pairwise <–> allDisjoint).
• Convert URIs to labels: new options allow the user control over where annotations are placed.

Bug fixes in Protégé-OWL

• Change entity URI(s): does not work with entities containing escapes in their URI.
• Import from file: gets the ontology URI wrong (uses the xml base instead).
• Move axioms: finish can be pressed when no target ontology selected.
• Open from URI: should not accept unless URI specified.
• Expression editor: expression cache doesn't update on switching active ontology.
• Edit | Create etc actions do not work correctly - label generation could be ignored.
• New classes are always asserted to be subclasses of owl:Thing if nothing else suggested.
• Disjoint properties: cannot add multiple disjoints.
• Axiom annotations: cannot roundtrip in RDF/XML.
• OWLAPI RDF/XML renderer: allDisjointClasses/rules with axiom annotation incorrect.
• Button "OK" in "Asserted class hierarchy" tab for property domain/range editor is disabled the first time the window is opened.
• SWRL: A(?x) ^ B(?x) -> C(?x) does not get parsed correctly.
• Editors in class creation dialog are in random order.

Enhancements in Protégé-OWL

• A URI preview is now shown in the new entity creation dialog.
• Tabs in the OWL class description editor dialog are now plugins. More information is available on the wiki.

Bug fixes in Protégé-OWL

• Fixed several bugs in the expression editor:
  • "Literal" is now correctly translated into rdfs:Literal instead of xml:Literal.
  • Underlining of syntax errors has been corrected.
  • Completion of multi-word entities should work even after a space.
  • Fixed a bug where the autocomplete popup was not showing on some Windows/Java combinations.
  • Autocomplete works even if nothing has been typed.
• Properties are now properly removed from the hierarchy when they are deleted.
• Warnings are now shown when duplicate multiword names are entered during new entity creation.
• Bundling an updated version of FaCT++ (1.2.2), which contains a fix for missing inferred property assertions.
• Encoding of output is now utf8 in OWLDoc.

Bug fixes in Protégé-OWL

• Fixed a bug where the inferred class hierarchy was being closed (and thus selection lost) on reclassify.
• The autoupdate download functionality now works for Linux users.
• Fixed a bug where all tabs fail to initialize if a plug-in with no ID is loaded.
• Fixed a problem with the InstallAnywhere installer that prevented the file.encoding system property from being properly set on the Mac OS.

Enhancements in Protégé-OWL

• A Beanshell plug-in is now available that allows users to write scripts to interact with the model/user interface from within Protégé-OWL.
• A Manchester syntax view is now available (shows the current selected entity), which is good for easy cut and paste into emails.
• Refactor | Copy/move/delete axioms... has been revisited such that you can select axioms by profile, e.g., EL++, and it is also now pluggable.
• There is a new Individuals by inferred type view.
• Load errors for some formats now provide more help with line numbers and allow you to view the sources.
• It is now possible to save as OBO 1.2 flat file format. This feature should be used with care. In particular:
  • Not everything in OWL can be represented in OBO format. Warnings are currently only reported to the console so please have this open when using this feature.
  • This was written using incomplete OBO documentation. We expect bugs and omissions and are interested in user feedback, so please try it and let us know what you think.
• There are several OWLViz updates:
  • Some global preferences have been moved into the File | Preferences | OWLViz menu.
  • Tracking view: OWLViz views (including plug-ins such as OWLPropViz) now allow a tracking mode which follows the current selection:
    • You can select the default mode for all OWLViz views in File | Preferences | OWLViz.
    • Some views allow you to turn this on/off locally using the view's Options button and selecting the Mode tab.
    • "Track selection" means that the global selection will be followed in OWLViz, making it good for using it as a navigation tool.
    • "Create graph manually" is the default behaviour, where you tell OWLViz which classes to show using the toolbar.
    • Providing a radius tells OWLViz how many classes around the current selection you wish to see.
  • Inferred view: nothing is only displayed as a subclass of Thing (no longer all classes making the view hard to read).
• Rename entity has been renamed (!) to "Change entity URI...".
• Change entity URI... allows you to select whether you wish to also rename puns.
• DL Query now provides result counts.
• Individuals by class view now gives membership counts.
• Custom tab layouts can now be removed.
• The changes plug-in has been updated to provide a simple axiom diff view to see the difference between two loaded ontologies. Note that this plug-in must be downloaded separately: http://code.google.com/p/co-ode-owl-plugins/wiki/ChangeView.

Bug fixes in Protégé-OWL

• Fixed a bug where an exception was raised if searching for datatypes.
• Fixed a bug where FaCT++ was not returning inferred domain and range information.
• Fixed a bug where an exception was being thrown when trying to accept auto-updates.
• Fixed a bug where it was possible to add multiple prefixes with the same name.
• Fixed a bug in the class hierarchy that was causing gaps to appear in the tree after drag and drop.
• Fixed a bug in the class hierarchy where selection failed in some circumstances.
• Individuals on the "Individuals by Class" tab are now sorted.
• dataOneOf now works in the expression editors.
• owl:Nothing and other unsatisfiable classes are now hidden in DL query results.
• owl:deprecated was added to standard annotation URIs.
• The export format can now be selected when saving inferred axioms.
• Local/web imports are now added to the recent locations list.

Changes & bug fixes in Protégé-OWL

• There is now an auto-update facility that can:
  • Let you know when new versions of installed plug-ins are available
  • Help you find and install plug-ins from within Protégé-OWL
  More information is available on our wiki.
• There is now an inferred object property hierarchy view.
• The new entity preferences have been tidied up and you can now choose / instead of #. More information is available on our wiki.
• The search/find preferences have been renamed to "General" and also include a setting for the expression editor delay.
• Usage allows you to turn on/off certain filters.
• Property and individual views show more inferred information.
• Updates to FaCT++ allow us to get inferred properties of individuals and domains/ranges of properties. Please note that FaCT++ for 64-bit Linux has not yet been updated.
• Bundling an updated version of the OWL API to allow fixes for several bugs.
• Fixed a bug where the General Axioms editor autocompleted with unnecessary : characters.
• Fixed a bug where the usage view broke in the presence of GCIs.
• Fixed a bug where individuals with the same name were disappearing.
• Fixed a bug where reasoners kept running in the background even when cancel was pressed.
• Fixed a bug where autcomplete would not work for the fillers of QCRs.
• Fixed a bug where the ontology annotations were not correctly handled when merging ontologies.
• Fixed a bug where find would not switch to an appropriate tab to display the entity.
• Fixed a bug in "Rename entities..." where tickboxes were ignored.
• Web link menu items (like those in the Help menu) are now implemented as plugins. More information is available on our wiki.
• The explanation/debugger has been removed from the default installation and will be available as a separate plug-in(s).

Changes & bug fixes in Protégé-OWL

• Individual ontologies can now be unloaded via the "Ontology source locations" dialog box. To access the dialog, choose File | Loaded ontology sources. Right-click on ontologies you want to unload and select "Close ontology" from the context menu.
• Individuals by class view now reflects ontology changes.
• Fixed a bug where the annotation editor would return an empty language in certain circumstances.
• Fixed a bug where subclass axioms with a description on the LHS would cause anomalies in the asserted class hierarchy.
• Fixed a bug in some lists where the edit button caused deletion.
• Fixed a bug where deleted entities still showed up in the finder and the new entity dialog.
• Fixed a bug where the general axioms editor added a : after axiom keywords (SubClassOf, EquivalentTo, etc.)

Enhancements in Protégé-OWL

• File associations now work properly, i.e., users can start Protégé-OWL by double-clicking on OWL files. Users of the OS X platform must perform an extra step for this to function - documentation for how to do this is available on the wiki.
• Axiom annotation is now possible. Documentation is available on the wiki.
• Expression editors now have memory. Expressions previously entered during the current session will be suggested as users type and will also be used for rendering.
• Ontology files that have changed outside of Protégé-OWL will be detected and users will be asked if they wish to reload them.
• The restriction editor now has support for datatype restrictions.
• The create class/property/individual dialog has been overhauled to provide feedback. Warnings about duplicate names and invalid input are now given at entry time.
• Bookmarks are now available when importing from the web.
• Move axioms selection strategies are now plug-ins.
• Merging ontologies now attempts to remove redundant imports statements.
• When duplicating classes, a dialog now prompts the user if the new statements should go into the active ontology or in the same places as the originals.
• Bundled updated versions of the OWL API and FaCT++.

Bug fixes in Protégé-OWL

• Protégé-OWL now shuts down correctly - all windows with unsaved work will prompt before allowing the application to exit (even with Command-Q on the Mac OS!).
• Windows users finally have an exit option in the file menu.
• Mac users will notice the application behaving more consistently:
  • Preferences and About are both in the correct menu.
  • The save indicator now appears in the close window button.
• Clicking on hyperlinks does not cause the annoying tab switch if the current tab is capable of displaying the linked object.
• The superclasses views have been fixed to sort out several update issues.
• Pellet only requires reclassification when logical axioms are changed - for example, adding annotations no longer requires reclassification for DL queries.
• Fixed several bugs in autocomplete:
  • Popup would get stuck on screen and could not be removed.
  • Highlighting parts of the editor text would cause problems.
  • The top level datatype (Literal) was not available and other datatypes were not in the list.
• Default bookmarks for opening ontologies from a URI work correctly again.
• Opening from a URI now prompts the user to open in the current or new window (also, the default has changed to current window).
• Fixed a bug where collapsing tree nodes caused odd selection behaviour.
• Reasoner errors are now presented to the user directly (inconsistent ontologies/non-simple properties, etc.).
• Fixed a bug in OWLViz that prevented it from showing most international characters including Chinese and many others.

The only change in this build is a fix for the ZIP file to install Protégé. The name of the directory where Protégé is installed still contained the text "alpha" instead of being updated to "beta" as it was in the platform independent installer program.

If you installed Protégé using InstallAnywhere, there is no need to upgrade to build 101.



Changes & bug fixes in Protégé-OWL

• The first time you install build 100, all preferences will be reset to their defaults. Sorry, but this was necessary to allow us to upgrade the way preferences are stored.
• Tab layouts are now stored with other preferences so that they will persist across installations.
• It is now possible to move all entity names captured in the URI to annotation labels. The URI fragments will be replaced with an Auto ID generated in accordance with your "New Entities" preferences. Try Refactor | Convert entity URIs to labels.
• Punning has been reinstated. Now, when creating new entities, the URI is checked against existing entities of the same type only.
• Fixed a bug preventing disjoint properties and some other axioms from appearing in the usage views.
• Multiple selection now works in the "loaded sources" page of the imports wizard.
• File | Open recent now asks if you want to open the desired ontology in the current frame or in a new frame.
• Tools | Create class hierarchy now takes into consideration the "New Entities" preferences.
• Links to Protégé 4 documentation now appear in the Help menu for convenience.
• Fixed a bug where lists (particularly list of individuals) were not being rendered with the correct font.