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Clearing Protege 4 Preferences

Protege 4 uses the Java Preferences API to store user preferences and activity. This allows for persistence of preference data across installations of Protege 4.x, e.g., recently opened ontologies, rendering preferences, location of Graphviz (used by the OWLViz plug-in), etc. The storage location of these preferences varies according to operating system:

  • Linux - stored in ~/.java/.userPrefs
  • Mac OS X - stored in ~/Library/Preferences/
  • Windows - stored in the Windows Registry at HKEY_CURRENT_USER/Software/JavaSoft/Prefs

Occasionally, users may need to clear the Java Preferences to fix errors displayed by Protege. Preferences can either be deleted manually, or via a tool called the Java Preferences User Interface. Read more about both options below.

Delete preferences manually

To manually delete Protege 4.x preferences, first determine the location that preferences are stored on your operating system. Locations are listed above in the introductory paragraph.

For Linux and Mac OS X, navigate to the appropriate location and delete the Protege preferences.

For Windows systems, delete the Protege preferences entry from the Windows Registry. To edit the Windows Registry, click Start | Run... and in the resulting Run dialog type "regedt32" and click OK. To follow is a screenshot of the Registry Editor with the Protege preferences entry visible:

Microsoft Registry Editor

Delete preferences using the Java Preferences User Interface

A perhaps nicer option, is to download the Java Preferences User Interface tool, which provides a user-friendly interface for updating and/or deleting preferences. After downloading, type the following on the command line:

    java -jar jpui-0.4.0.jar

To follow is a screenshot of the resulting JPUI application with the Protege preferences entry selected:

Java Preferences User Interface

To delete the preferences, select PROTEGE_PREFERENCES and choose Node | Delete from the top menu bar.

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