The contents of this page describe changes relative to the Protégé 3.3.1 release and the Protégé 3.4 beta series.



Bug fixes in Protégé-OWL

• Fixed a bug introduced in a previous build that prevented users from seeing newly created properties if "Create label" is unchecked on the Preferences | New Entities tab.

New features in the Protégé-OWL editor

• Added finer control over the naming of new entities, including automatic ID generation. This is described in more detail on the wiki.
• Created a wizard to selectively move axioms (Refactor | Move axioms to ontology...). When multiple ontologies are loaded, there are several strategies to select sets of axioms that can then be moved from one ontology to another, e.g., move all disjoint axioms, move all axioms referencing a certain class or classes, move all labels, etc.
• Implemented an action that removes all of the disjoint axioms that reference subclasses of a selected class (Edit | Remove disjoints for subclasses...).
• Fixed and re-enabled the export of OWLViz diagrams to PNG and JPG.
• Changed the the default path to the dot executable for OWLViz on Mac OS X to correspond to the current distribution (/usr/local/graphviz-2.14/bin/dot).
• Implemented a timestamp for debugging, accessible from Window | Timestamp log/console.
• 64-bit Linux support for FaCT++ has been added.

Bug fixes for the Protégé-OWL editor

• Fixed a bug that was causing DL queries to ignore changes in the ontology since the previous classification.
• Fixed multiple rebuilds of rendering caches (therefore speeding startup with large ontologies).
• The order of languages specified in the annotation renderer is now correctly respected.
• Optimized the painting of most views (using framelists - such as the Class Description) to speed up responsiveness.
• Corrected multiple bugs in the caches that caused old names for entities to be retained in searches/expression editors and views to ignore updates when the labels were changed (including the annoying bug in trees where the new name got cut off if it was longer than the old name).
• Inherited anonymous classes pick up defined classes correctly (i.e., now shown for equivalent class axioms on ancestors).
• Reasoner errors should be more visible to users now. In particular, Pellet now throws an exception if unsupported axioms are used in your ontology (rather than silently stripping these out).
• Search now finds anything starting with the search string, regardless of whether it is rendered with ' escapes (for names with spaces).
• It is now possible to cancel a close if ontologies are unsaved.
• Individual editors tidied up and now available for sameAs and differentFrom assertions.
• Editing of disjoint axioms is now possible (and with a multiselect tree or a comma separated list syntax, sets of classes/descriptions can be added).
• Work has been done to ensure consistency between expression editors so that they all use the same parsers.
• Multiple selection now reinstated for individuals (to allow deletion, etc.).
• Partially fixed a bug where OWLViz was failing to layout graphs when accented characters were used in the names of things. Support for Latin Extended A, Latin Extended B, and Korean characters was added. We would appreciate feedback as to which other character sets should be supported - in particular, if you are able to help us check that a particular set works, that would be very useful.
• Changes to the ontology libraries are now saved when OKed and ignored when cancelled.
• Selecting the location from which to load a new ontology no longer ignores the user input when a bookmark is selected.
• Fixed "duplicate class" dialog exceptions on cancel.
• Look & feel options on the command line are no longer ignored.
• Ontologies menu cleaned up (including correct updates on ontology name changes).
• A new version of the OWL API was bundled that fixes several Manchester OWL Syntax issues.

Changes & Bug Fixes in Protégé-OWL

• Added an "Ontologies" menu to facilitate the following:
  • The active ontology can be chosen from the menu (as an alternative to the dropdown), making it more accessible.
  • Provides different strategies for determining the active ontologies, i.e., the ontologies whose contents are visible in the editor and get sent to the reasoner. The default setting is "Show the imports closure of active ontology" as it always has been, but the user can also choose:
    • Show only the active ontology (useful for checking that an ontology contains only the statements it should)
    • Show all loaded ontologies (sometimes some ontologies are not in the imports graph)
• Active ontologies are now highlighted in the OWLViz imports graph. Double-clicking an ontology makes it the active ontology.
• New customizable tabs can be created and shared with other users. Select Tabs | Create new tab..., give it a name, and then add whichever views you want. When you select Tabs | Save current layout, or close Protégé, the layout will be saved and available the next time the application is started. You can also distribute the layout by sending someone the configuration file. The file is located in the Protégé installation directory under Data/View Configurations/ and will be named something like "viewconfig-custom-MyTab.xml". Just have your friends copy this into their Data/View Configurations/ directory and as long as they have the required view plug-ins, the tab will pop up as available in their Protégé installation.
• Ontologies are now sorted in the imports wizard.
• The default heap size was increased to 200M.
• The Inferred Superclass view is now updated when a reasoner is selected or classification is performed.
• Named inferred equivalents now show up correctly in the Class Description view.
• Users will now get a warning message when trying to open an ontology with the same URI as the one already loaded (in the same window).
• Close windows behaviour was made more consistent.
• Drag and drop exception on Mac OS X finally destroyed. Yippee!!
• A bug that caused FaCT++ to continuously reclassify was fixed. This was occurring when FaCT++ threw an exception during classification and meant that subsequent calls to the reasoner caused reloading and reclassification. It was most noticeable in drastic slowdown of navigating the inferred hierarchy.
• Fixed a bug where FaCT++ didn't like disjoints containing one class.
• Bundling an updated version of the OWL API to include fixes for property chain syntax changes (OWL 2.0).

Changes & Bug Fixes in Protégé-OWL

• The "Usage" views can now be filtered (see File | Preferences | Usage) to remove disjoint and simple subclass axioms where the classes on both sides are named. This should make the views less cluttered. Filtering is off by default.
• All lists of ontologies have been tidied up to render more consistently (by short name) and are sorted to make finding the correct ontology easier.
• A refactoring action for converting min cardinality 1 restrictions to someValuesFrom restrictions is now available.
• Additional rendering preferences allow a combination of an annotation renderer, but with prefixes. This should help resolve ambiguity in the interface.
• Bundling an updated version of FaCT++ (the imminent 1.1.12 release) to solve several bugs, including min cardinality 0 and data facets on floats. This version of FaCT++ now also supports 64-bit editions of Windows.
• Bundling an updated version of the OWL API to solve several parser errors (particularly those with datatypes and properties).
• Right click menu on the class description view now functions correctly.
• Internationalization on dialog button labels now works.
• Pellet now updating on reclassify when ontology has changed.
• Property (role) chain parser now accepts more than 2 elements.
• Removed bug where axioms were getting crossed out.
• Floating views now show the selection correctly (previously they were blank).
• Proper screen refresh when closing views.
• Editor in general axioms view now partially implemented.
• Old views for which the "Cannot load" gray button of despair appears can now be closed.
• Annotations can now be copied when "duplicate selected class" is called.
• Editing the features of properties in the property description view now works for all sections.
• The search box does not magically disappear for those users lucky enough to have a tiny little screen.
• Equivalent classes now show in the class hierarchy.
• Ontologies that have been loaded from the Web can now be saved to disk (rather than the save being ignored).
• The individuals view now has tooltips for the full URI of the individual.
• Carriage returns (generated by Windows) are now correctly ignored in expression editors (such as DL Query).
• Canceling rename operations is now possible.
• When creating annotations, user are no longer limited to the languages hard-coded in the dropdown (which is now editable).
• Property trees are now sorted alphabetically for ease of navigation.
• (rdfs)Literal - the top datatype - is now accepted by the expression editor.
• Fixed a bug that prevented button icons from showing up in the OWLViz tab.

Changes & Bug Fixes in Protégé-OWL

• This build was generated with a new version of InstallAnywhere, which fixes an exception (java.lang.NumberFormatException: For input string: "0-b19") being thrown when users try to install and/or uninstall Protégé.
• The name of the executable file for the Protégé installer has been changed from "install_protege.exe" to "install_protege_4.exe". A number of people are using both Protégé 3.4 and Protégé 4 and asked that the installer executable for the different versions have different names.
• Bundling a new version of the OWL API (version 2.2.0), which fixes a parser crash when there are missing imports.
• Users now have the ability to render entities using an annotation value of their choice and may also specify the default language. These options are configurable via the File | Preferences dialog on the Renderer tab.
• "Usage" views no longer throw exceptions when no entity is selected.
• The Manchester OWL Syntax Parser now handles renderings with spaces.
• The expression editor is now inside of a scroll pane.
• The default directory for Graphviz (used by OWLViz) for Windows machines was upated to C\:\\Program Files\\Graphviz\\bin\\dot.exe.
• Fixed a problem where a "blank" superclass is added to a class if add covering axiom is selected when a class with no asserted subclasses is selected.
• The "Resolve missing import?" dialog no longer appears after enabling the Inferred Axioms view.
• Fixed a problem where users can create nameless classes using the Tools | Create Class Hierarchy wizard if blank lines exist in the input.
• Cut-and-paste now works with entity annotations.
• The process of merging ontologies into an exisitng ontology is no longer missing the step that allows users to specify the existing ontology.
• Fixed some problems handling class hierarchies containing loops. In particular, ontologies such as BIRNLex can now be viewed properly.

Changes in Plug-ins

• A new View plug-in entitled "Annotation Search" is available for download from the CO-ODE project's Web site. The plug-in allows users to search entity annotations for a string or regular expression match.

Changes & Bug Fixes in Protégé-OWL

• Fixed a bug that caused FaCT++ to crash if the active ontology was changed.
• Fixed a bug that caused Pellet to throw exceptions when the active ontology was changed.
• Wildcard search is now supported in entity views.
• The "Gather ontologies" dialog box now has a scrollbar for the list of ontologies.
• Fixed a bug that prevented the Inferred Axioms view from loading.

Changes & Bug Fixes in Protégé-OWL

• Disabled reclassifying when the active ontology is switched.
• Fixed a bug that caused individuals to disappear.
• Fixed a bug where only a single annotation for each URI was being shown in the annotation view.
• Bundling a more recent OWL API (version 2.1.1).

Changes & Bug Fixes in Protégé-OWL

• The Protégé-OWL editor is now more tolerant of OWL Full style imports where the name of the imported ontology does not match the name of the ontology used in the imports statement. When an import is broken, the editor makes a best effort attempt to load the correct ontology. The broken import is highlighted and an option to fix the import is suggested.
• It is now possible to add Self and Data restrictions.
• Fixed some problems with refreshing the user interface when changing the style of entity rendering.
• Added a context menu to the Ontology Metrics view that allows users to launch a dialog that displays the axioms included in an axioms count. To display the dialog, right-click any item in the metrics view that with an axioms count (for example: Disjoint classes axioms count) and choose "Show axioms".
• Added an option to auto-expand the class tree when an ontology is opened. The auto-expansion depth is configurable via File | Preferences... | Tree preferences.
• Fixed several problems with the display of individuals, including a refresh problem in the Individuals tab that occurred when switching between ontologies.
• Fixed a bug that caused some class expressions to contain strike-out text.

The only change in this build is a recompiled version of a FaCT++ JNI library. The library in the previous build was causing problems with FaCT++ on older versions of the Mac OS.



We have made a significant change to the plug-in architecture in this build. The existing Java Plugin Framework was replaced with the OSGi framework. OSGi is gaining traction in industry and, in particular, has been adopted by the popular Eclipse Language IDE and Rich Client Platform. The advantages of using the OSGi framework include:

• the stability of a plug-in framework that is industry standard and has reference implementations developed and used by companies such as IBM
• the ability to extend Protégé by adding existing OSGi bundles
• the availability of a plug-in framework that can easily be used by applications that have graduated beyond being just a Protégé tab

To use the new framework, plug-in developers will need to modify their MANIFEST.MF and plugin.xml files. Code changes are not generally required. Instructions for how to modify a plug-in to fit the new framework are available on the Protégé Wiki.

Bug Fixes in Protégé-OWL

• Bundling a new version of FaCT++, which fixes a bug that was causing Protégé-OWL to crash when using the DL Query tab.

General

• Added apple.laf.useScreenMenuBar=true to the Protege.lax file so that Protégé uses the screen menu bar on the Mac OS.
• Added entries in the Protege.lax file for lax.nl.java.option.java.heap.size.initial and lax.nl.java.option.java.heap.size.max. Values for the initial and max heap sizes are set at 200M initially, but can be modified by users directly in the LAX file. Further instructions for setting the heap size in Protégé are available on the Wiki.

Changes & Bug Fixes in Protégé-OWL

• Bundling a more recent OWL API (Subversion revision number 455).
• Bundling a new version of FaCT++ (version 1.1.9, which supports floating point datatypes).
• Added the ability to save ontologies in the Manchester OWL Syntax format. This functionality is accessible via the File | Save as... menu item.
• Fixed a problem that prevented individual property axioms from being asserted and edited.
• Fixed a problem with the Pellet connection. Ontology updates are now reflected in reasoner results.
• Fixed a problem with the repository mechanism.
• Improved explanation and reasoning support.

Bug Fixes in Protégé-OWL

• Fixed some problems that were preventing the direct in-memory connection to FaCT++ from working in the previous build (build 51).

What's included?

An exciting new version of the Protégé-OWL editor, developed by our collaborators at the University of Manchester.

New features in the Protégé-OWL editor include:

• Built on top of the OWL API. Large ontologies such as the NCI ontology can be loaded in around 500M of memory.
• Support for OWL 1.1 (qualified cardinality restrictions, property chains, disjoint properties, self restrictions, user-defined datatypes, reflexive, irreflexive, and antisymmetric properties, etc.).
• Support for loading ontologies in RDF/XML, OWL/XML, OWL Functional Syntax, KRSS, and OBO Flat File format.
• Direct in-memory connections to Pellet 1.5 and FaCT++.
• Preliminary support for the explanation of entailments.
• Hyperlinking for classes, properties, and individuals when browsing ontologies.
• Dynamic usage views which allow the usage of any class, property, or individual to be seen instantly while browsing the ontology.
• Support for editing multiple ontologies:
  • Axioms can easily be pulled from one ontology to another.
  • Tolerance of missing imports.
  • Automatic mapping of locally stored ontologies when resolving imports.
• DL Reasoner query tab for asking standard DL queries.
• Improved keyboard navigation.

There are several additional plug-ins for the Protégé-OWL editor, available for download from the University of Manchester's CO-ODE website.

What's not included, but coming soon?

• Protégé-Frames editor
• Protégé Services
• Protégé Web client
• New Plug-in Architecture