Protege 5.0 Beta Release Notes

Protege Desktop 5.0 Beta

Enhanced search capabilities at work in Protege Desktop 5.0 Beta

We are very pleased to announce Protege Desktop 5.0 beta!

For Users:

• Download and installation instructions.
• Submit feedback, questions, and/or bug reports on the Protege User Support mailing list. Sign up for the list at the Protege website.
• Read Protege Desktop documentation.
• Join the Protege community on Facebook and Twitter.

For Developers:

• Access the source code, file issues, and submit pull requests on GitHub: http://github.com/protegeproject/protege.
• Learn how to build a distribution from source.
• View example code for developing tab, view, and menu plug-ins.
• Contact us with your questions on the Protege Developer Support mailing list. Sign up for the list at the Protege website.

Release Notes

All newer Protege release notes have been moved to github.

The contents of the release notes section describe changes relative to Protege 4.3.

Build 5.0.0-beta-12 (2014-May-30)

• Removed the Java "-server" option from the Protege run scripts. This option caused the run scripts to fail on systems that only have a JRE installed vs. a JDK (#51).

Build 5.0.0-beta-10 (2014-May-28)

Enhancements

• Moved the Protege Desktop source code to GitHub to allow for easier collaboration with developers outside of Stanford.
• Moved the Protege Desktop build system to Maven to standardize the build process.
• Upgraded to Java 7.
• Upgraded to the latest version of the OWL API (v3.5.0).
• The search functionality has been significantly improved to search annotation values, display names, entity IRIs, and logical axioms (previously only display name was searched).
• The Individuals tab now filters the list of individuals displayed based on the selected class in the class hierarchy (#1).
• The UI no longer allows specification of owl:real as the type for a literal (#37).
• Entering a number into the OWLConstantEditor now parses the value and chooses the correct datatype if no datatype was specified (#42).
• Exporting DisjointClasses axioms is no longer enabled by default, as this can be an expensive operation (#43).
• Auto-update only checks for updates once per day, rather than checking for updates every time Protege launches (#45).
• The Active Ontology tab now shows ontology metrics by default (#46).
• Renamed labels in the DL Query tab plug-in to be clearer and more standard (#1)
• Definition annotation properties are now listed after label annotation properties, making the Annotations view more user-friendly for the bio-ontology community (#47).
• Added the ability to view axiom annotations inline (accessible via View -> Display axiom annotations inline). Previously, it was necessary to click the @ symbol to bring up a separate dialog for viewing inline axiom annotations (#50).
• Added an option to toggle rendering of annotation datatypes in the Annotations view (accessible via View -> Display datatypes on annotation values).

Bug Fixes

• The inferred object property hierarchy no longer displays owl:bottomObjectProperty as a leaf of every node (#9).
• Selecting classes in the class hierarchy will only request directly inferred individuals from the reasoner. Previously, Protege requested both direct and indirect inferred individuals, which caused performance issues with larger ontologies (#15).
• Fixed a bug in the auto-update functionality that caused exceptions when encountering plug-ins with invalid version numbers (#18).
• Fixed a typo in the DL metrics view (#20).
• Modified the UI of the Automatic Update dialog to prevent display of an unnecessary trailing '.' character on plug-in version numbers (#23).
• Fixed an issue that occasionally caused a NullPointerException when opening ontologies (#34).
• Fixed an issue that occasionally caused the Continue button to remain disabled on the Export Inferred Axioms dialog (#36).

The installers and release notes for previous Protege desktop version are available here.