P4 1 Release Announcement

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Protege 4.1 Release -- July 26, 2011

Protege 4.1 screenshot

We are very excited to announce the 4.1 release of the Protege-OWL Editor!


Release Highlights

This section describe changes relative to Protege 4.0.2.

... and much more! Please refer to the complete set of release notes below.

Useful Links

Complete Release Notes

This section describe changes relative to Protege 4.0.2.


  • Bundling the new OntoGraf visualization plug-in with the default installation. OntoGraf is accessible as a tab via the Window | Tabs menu, or as a view via the Window | Views | Class views menu. Thanks go to Sean Falconer for this contribution.
  • Protege's ontology repository mechanism is now implemented according to the XML Catalogs specification from the OASIS open standards group.
  • Added a basic explanation feature. Many inferred assertions now have a clickable question mark icon nearby, which will display a simple explanation dialog.
  • The manner in which reasoners are started was simplified. Selecting the reasoner and choosing to classify the ontology are now divided into separate steps. New reasoner preferences were also added, including fine-grained control of what classification steps take place during a classify operation.
  • Bundling an updated version of the OWL API (3.2.3).
  • Simplified and consolidated some of the menu items in the main menu bar.
  • Made rendering preferences much quicker to access via the new "View" menu, e.g., View | Render by name, View | Render by label.
  • Axiom annotations are now displayed in axiom tooltips.
  • Added support for the disjoint union axiom.
  • When parsing errors occur, Protege closes all file handles. Users of the Windows platform can now edit malformed ontologies in external applications, then reload the ontologies in Protege without having to close the Protege application. This already worked on other non-Windows platforms.
  • Dublin Core annotation properties are no longer included by default in new ontologies. If users want Dublin Core annotation properties, we recommend you import protege-dc.owl.
  • Modified the user interface of the dialog for creating/editing annotations to disable the "Lang" combo box if a type other than plain literal is selected.
  • Users can now enter inverse object properties when adding object property disjoint or equivalent axioms.
  • After a user runs a reasoner, Protege will now display inferred same individuals and disjoint classes. The display of inferred disjoint classes is turned off by default.
  • If a user edits a general class axiom (GCI) in the "General class axioms" view in such a way that it became a regular class axiom, Protege will present a dialog after completion of the edit to notify the user that the GCI is now a regular class axiom and will be displayed in the appropriate view (not the GCIs view).
  • Assertions that an individual has a certain type can now be deleted from the class description panel for said type.
  • The asserted and inferred class hierarchies are now synchronized for class selection.
  • The class members list view is now aware of imports.
  • Protege now lets you specify the prefixes that are used in an ontology.
  • Protege now uses a recursive search starting at the working directory to find on-disk versions of ontologies to import.
  • Provided new user interface mechanisms to give users the ability to edit ontology repositories from within Protege.
  • Added explanation support for the DLQuery plug-in.
  • It is now possible to add annotation values that are IRIs that do not correspond to any known entity.
  • The merge ontologies functionality no longer includes the merged ontologies as imports.
  • Modified the installer program to add a new item to the program group on Windows called "Protege (advanced start)". Clicking on this program group item will launch Protege using the "run.bat" file in the root directory of the Protege installation.

Bug Fixes

  • Axiom annotations are no longer lost when an axiom is changed.
  • Fixed a NullPointerException that occurred when using the imports wizard to import anonymous ontologies.
  • Fixed a problem where the create class hierarchy tool (Tools | Create class hierarchy...) did not respect the preference that new entities should be created with a particular URI.
  • Made qualified name rendering consistent when a user moves between ontologies in a workspace. This is done by calculating a merged prefix name to prefix map for the entire workspace that doesn't change when switching active ontologies.
  • Declarations are no longer copied from imported ontologies to importing ontologies on save.
  • Fixed a bug that allowed Protege to create empty disjoint/equivalent axioms. These axioms asserted that a class, object property, or data property was disjoint or equivalent to something, but no other entity was mentioned. A similar problem existed for same and distinct individuals.
  • Fixed the misspelling of the NMTOKEN data type.
  • Removed extra owl:topObjectProperty and owl:topDatatypeProperty super-property when creating new properties.
  • Fixed a relative URL problem that prevented users from moving an ontology repository (in the form of a catalog.xml file) from one directory or machine to another.
  • Fixed a rarely occurring bug where files with international character sets were not being correctly saved.
  • Made several improvements and fixes to the process of exporting inferred axioms, including a progress monitor, improved performance of the inferred disjoint classes, and better management of the OWL reasoner.
  • Fixed a problem where Protege was making the facet value for a data restriction, e.g., int[>= 3], have the string type rather than the appropriate type, which caused trouble with reasoner plug-ins.
  • The application startup process was significantly improved. Previously, some users were getting exceptions when they started multiple instances of Protege, and had problems when running different versions of Protege at the same time.
  • Fixed a bug that caused new users to have their font inadvertently set by the renderer preferences panel.
  • Imports of anonymous ontologies no longer fail.
  • Fixed a serious data loss bug that occurred when users double-clicked on OWL files to open in Protege.
  • Fixed an issue with the rendering preferences that was making it difficult to see ontologies rendered with rdfs:label.
  • Fixed a bug that caused the list of active ontologies to be incomplete in some cases.
  • Fixed a bug that prevented SWRL built-ins with variable numbers of arguments from being used.
  • Fixed a bug that in some cases caused a case-insensitive search to be case-sensitive.
  • Fixed a problem with the installer that caused empty program groups on Windows 7.
  • Fixed a problem that prevented the uninstaller from working properly on 64-bit Windows 7 machines.
  • Fixed a problem with the installer program that caused broken application bundle files on the Mac OS.
  • Made a small configuration change to fix a serious performance problem with the OS X application bundle.
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