Protege 3.5 Release Notes

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Protege 3.5 Release -- April 24, 2013



Note to all users: Protege 3.5 requires Java 6.

Note to users of Mac OS X 10.7.5 and above: The default Gatekeeper settings for Mountain Lion are to only allow application downloads from the Mac App Store and identified developers. The Protege software does not carry "identified developer" status, and you may see an error when attempting to download that the installer file is "damaged and can't be opened". To successfully download the installer file, navigate to Apple menu | System Preferences… | Security & Privacy | General tab, and select "Anywhere" from "Allow applications downloaded from".


Release Notes

This section describes changes relative to Protege 3.4.8

Core Protege

  • Dialogs are now centered in the main window.
  • System slots can now be selected for export to CSV in the Query Tab.
  • Fixed a bug that prevented the Finish button from being enabled when creating a database project.

Protege-OWL

  • When running in client-server mode, the Protege native writer export is now done in a more efficient way on the server. The performance increase should be significant, especially on slow networks.
  • Fixed a bug in the Protege native writer that prevented some untyped resources from being exported.

SWRL

The SWRLTab now supports the Drools rule engine. A new tab called the SWRLDroolsTab provides a graphical interface for interacting with this implementation. The existing SWRLJessTab is still available. All existing SWRL built-in libraries are supported in the Drools implementation. Both the Drools and Jess implementations now use a pair of OWL 2 RL-based reasoners for performing inference (read more). These reasoners are also used by the SQWRL query language. The Java APIs provided by the SWRLTab have changed slightly so users of these APIs will need to update their code. Information on these changes can be found here. The process of building the SWRLTab and its associated rule engines has also changed. The new build process is outlined here.

BioPortal Import Plug-in

Made significant enhancements to the BioPortal Import Plug-in:

  • Users may now search for terms in all BioPortal ontologies, and navigate to a specific BioPortal ontology to import branches of the class tree.
  • Added the ability to start multiple import processes at the same time.
  • Importing is now done in separate threads, and can be canceled at any time by the user.
  • Added a progress dialog to show import progress.
  • Users may now specify a BioPortal API Key in the BioPortal Configuration dialog (accessible from BioPortal | Configure... | General). This allows access to private ontologies for which users have an API Key.

Collaborative Protege

Users may now add the collab.precache.notes.count property to the protege.properties file for controlling whether or not ontology notes are precached. If set to false, no precaching is done. This improves the start up time of Protege clients for projects that have large numbers of notes.

Read more about Collaborative Protege.

Change Management

Added Java utilities for exporting changes and notes as CSV files. Source code and export scripts are available in our Subversion repository.

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