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



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