The contents of this page describe changes relative to the 3.3.1 release of Protégé.



Changes & Bug Fixes in Core Protégé

• Added search support for multiline string values in the Protégé user interface and in the Protégé API.
• Fixed a bug where duplicate child nodes appeared in the class tree (or any other tree that uses LazyTreeNode). Many thanks go to Bob Dionne for the fix.
• Protégé now escapes the slot and slot value delimiters in the query results file exported from the Queries tab. Again, thanks go to Bob Dionne for the fix.

Changes & Bug Fixes in Protégé Client-Server

• Disabled the compression algorithm for client-server communication. We have encountered occasional problems in certain configurations with clients hanging because of the compression code. We are currently investigating this issue.
• Fixed some refresh problems when an entity (class, property, individual) was renamed in the user interface.
• The insertion order is now preserved when calculating the value closure for slots.
• Fixed some issues with inherited browser slot patterns. In previous versions, the browser slot patterns were not always inherited by subclasses.
• Fixed a problem that prevented preservation of default view annotations.

Changes & Bug Fixes in Protégé-OWL

• The restriction editor finder now uses the same finder as the class tree. This means that users will no longer have to add a "*" in front of the search string.
• Fixed an exception was sometimes thrown when a disjoint class was removed in the user interface.

Changes in Collaborative Protégé

• Rename events now are shown as one aggregated change in the Changes tab and the collaboration panel.
• Added more checks to determine an absence of changes and to determine if the annotations project is present in the changes and annotations API.

Changes in Core Protégé

• Made several performance optimizations for the client-server mode, namely that RMI can compress data before sending it over the wire. More information about configuration settings for the Protégé server are available on the wiki.
• Added debug and performance monitoring support in the Protégé logger for client-server mode. More information is available on the wiki.

Changes & Bug Fixes in Protégé-OWL

• Optimized performance of the OWL Individuals tab (not the Instances Tab!) in client-server mode for classes with large number of individuals that have browser slots configured. The MultiResourceWidget now uses a different structure for retrieving property values from the server that contains among other things, the individual and the browser text. This means that computation of the browser text can now be done on the server, thus preventing multiple calls across the network. Performance of the OWL Individuals tab is also much improved by using the compression mentioned above. Finally, we optimized several parts of the UI code to minimize the number of network calls.
• Added a fix for possible name conflict problems at parse time (e.g., if you import an OWL file into a OWL database) by using a random number generator for the anonymous class and individual names.
• Added a fix for the native writer that saves each import with its own namespace.
• Creating a subproperty will now create a property that has all the types of the super-property.
• Fixed several refresh problems in the UI that occurred after renaming an entity (this applies to both Frames and OWL), changing the range of a datatype property, etc.
• Fixed a problem in the OWL Properties tab that made properties appear twice when designating a property as functional.
• Fixed some memory leaks when disposing a project.
• The Add type button in the OWL Individuals tab is now disabled if no individual is selected.
• Fixed some bugs that could involve data loss, including a) values of sub data properties can be lost when an OWL ontology is parsed, and b) database import of projects with individuals can become corrupted.

Changes in Standard Extensions

• The EditorPaneWidget now supports text highlighting and insertion of internal links to entities in the ontology (e.g., when clicking on an internal link for class "Pizza", a window will appear showing class details for Pizza).

Changes in Collaborative Protégé & the Changes Tab

• The Changes and Annotations Ontology (ChAO) used by the Changes Tab and Collaborative Protégé to store change tracking and annotation information can now be stored in a database. We have documented how to convert an existing ChAO from the RDF file-based back-end to the database back-end on the wiki.
• The same ChAO project can now be shared by more than one project. For example, the CollaborativePizza and CollaborativeNewspaper projects may share the annotation_PizzaNewspaper.pprj project. There is also no longer a requirement that the ChAO project name start with "annotation".
• When a user enables the Changes Tab for the first time, she will be asked what type of ChAO project she wants to create. She can choose between:
  • RDF back-end (previous setup and default option)
  • Database back-end
  • Associate an existing ChAO project
• The Change menu has several new items:
  • Show Changes Ontology Details (e.g., location, back-end, number of annotations and changes)
  • Browse Changes Ontology
  • View Change Statistics and Conflicts (e.g., the editing conflicts between users)
• A new Changes and Annotations API provides full access to the changes and annotation instances stored in a ChAO knowledge base. We have documented this new API on the wiki.
• It is now possible to extend the set of existing annotation types (Comment, Advice, Proposal, etc.) from ChAO with custom annotation types, simply by creating a subclass of the Annotation class in the ChAO project. You may add your own properties/slots to the new annotation type and customize its user interface form. Collaborative Protégé will automatically pick up this new annotation type and show it in the available annotation types combo box in the user interface.
• All annotations defined in ChAO now have a subject slot attached to them. An automatic backwards compatibility fix is provided for previous versions of the ChAO.
• The forms for annotations in ChAO have been updated to more closely resemble a send email form. Users may now enter HTML styles in the body of the annotations and internal links to entities in the ontology.
• The creation of annotations will show a dialog that will allow users to post or cancel a message. In previous versions, when the user clicked on the create annotation button, a new annotation was created automatically. Now users have the chance to cancel submission of the new annotation.
• All annotations are now rendered with a type specific icon so that they can be more easily distinguished in the user interface. For example, a comment will have a little "c" in its icon, a proposal will have a "P", and so on.

Please note: We strongly recommend that users of the Protégé-OWL editor upgrade to this build, which contains a collection of very critical bug fixes.

Changes in Core Protégé

• There are some new startup options that allow Protégé clients to connect directly to a Protégé server:
  •  -server.user=xxx
  •  -server.password=xxx
  •  -server.host=xxx
  •  -server.project=xxx
• Introduced code generation capability for Protégé-Frames, accessible from the "Code" menu. Works with both file and database back-ends.
• Added support for the Derby database (many thanks to Mike Smith!!).

Bug Fixes in Protégé-OWL

• Fixed a bug in the parser that could lead to data corruption in a small number of cases for OWL ontologies that contain metaclasses.
• Fixed an issue that could silently cause data corruption when using the native writer in combination with sorting ontology contents.
• Fixed an issue with the native writer choosing the wrong file encoding for imported files. This sometimes caused data corruption when the imported files contained UTF-8 characters.

Changes & Bug Fixes in Core Protégé

• Fixed a memory leak in the database mode.
• Removed dependencies on the "looks.jar" file. Applications that only use the Protégé APIs no longer need to include looks.jar on the classpath.
• The default column types for MySQL in the database backend are now VARCHAR(500) with UTF-8-BIN collation. This means that the database backend will work with entity names longer than 255 characters and several problems have been solved related to ontologies that have two entities with identical names - one capitalized and one with small letters.
• In the Queries tab, the export functionality now quotes values if delimiters are used in slot values.
• Various fixes for events in the client-server mode.
• Added utility methods for managing projects on the Protégé server.
• Fixed a problem with the Frames HTML export functionality related to the export configuration file not being found.

Changes & Bug Fixes in Protégé-OWL

• The SWRLTab has been updated to be compatible with Jess version 7.1p1. Compatibility with Jess version 7.0p2 has been maintained.
• Fixed a bug in SWRL's rule group handling.
• Implemented some memory and performance improvements in the Protégé-OWL parser.
• Fixed an owl:Enumeration parsing problem.
• Added a "merging imports" mode to the Protégé-OWL parser that can be invoked programmatically (default is off), which means that all imports will be merged into one ontology. This feature can be used (if desired) when converting a file-based OWL model to the database backend. In this mode, all imports will be part of the same database table. This is also the way imports used to work prior to build 500 in the 3.4 beta series.
• Several fixes for the Protégé-OWL code generator. The generated getXYZ(String name) methods in the factory will return null if the name of the individual passed as the argument does not have the right ontology type.
• Several fixes for the Properties tab, namely that when users create inverse properties, domain and range information is not inverted as well.
• Added an addRepository() method in the OwlProjectFromUriCreator, which can be set prior to parsing.

Changes in Bundled Plugins

• The Jambalaya visualization plug-in has been updated to version 2.7.0, which has many new features and improvements. Searching has never been easier with a new quick search toolbar at the top of the view to help users find classes and instances. Jambalaya also now supports a document management system which lets the user associate documents or URLs with individual nodes. As a result, if there are any files, images, websites etc., that are related to a class or instance, the user can quickly preview those documents embedded right inside Jambalaya. Other new features include more support for custom node shapes, colors, borders, and images. Visit the Jambalaya website for a full list of all the new features and to peruse the user manual.
• Bundled an updated version of the Protege Script Console (build 0.32), which is a tab that provides a scripting environment within Protégé for manipulating an ontology.

Please note: We strongly recommend a clean reinstall of this build. A "clean reinstall" means that you should either a) install this build into an empty directory, or b) uninstall the previous version before installing build 504.

General

• This build contains some critical fixes for the client-server mode as well as Protégé-OWL's database back-end. If you use either of these, we recommend upgrading to this build.
• Users of the client-server mode need to edit the metaproject after upgrading to this build. Please ensure that all users are in the "World" group. The reason for this is that we have added enforcement for the Read and DisplayInProjectList policies. If a user is not in the World group, then the default policy will not allow them to view the ontologies on the server.
• We have made it possible for users to customize the database schema used by the database back-end. This will allow users to configure databases that are not supported by Protégé and to modify the current schema format to suit their needs. We are working on a wiki page that will document how to do this (but, it's not done yet...). If you want to do this before the wiki page materializes, please send us a message on one of the Protégé mailing lists.

Changes & Bug Fixes in Protégé-OWL

• Upgraded to Jena 2.5.6, which fixes some SPARQL query problems.
• The parser uses a new algorithm to compute orphan classes. This fixes the cases in which certain classes did not show up in the classes tree.
• The SWRLTab now works with the OWL database back-end.
• Improved the performance of the OWL file to OWL database conversion.
• Implemented some performance improvements for Protégé's client-server mode for the OWLClasses and Individuals tabs.
• Fixed a problem in the conversion of projects from one storage format to another.
• Fixed a problem with the OWL Wizard for creating multiple individuals.

Changes in Bundled Plugins

• Upgraded to version 1.3.1 of the DataMaster plug-in, which contains some minor bug fixes and improvements. Please see the DataMaster 1.3.1 wiki page for more details.

Please note: If you are a Protégé-OWL user, we strongly recommend a clean reinstall of this build (i.e., install into an empty directory, or uninstall the previous version) due to upgrades to the Jena and Pellet JAR files. There is also a very significant bug in the restriction editor in build 500 that can lead to ontology corruption.

Changes & Bug Fixes in Core Protégé

• Fixed a bug in the database back-end, which prevented users from working with Microsoft SQL Server.
• Added methods in ProjectView for reloading only one tab, or reloading all tabs except one.

Changes & Bug Fixes in Protégé-OWL

• Fixed a serious bug in the restriction editor that could lead to ontology corruption.
• Upgraded to the 2.5.5 version of Jena.
• Upgraded to the 1.5.2 version of Pellet (used by the direct reasoner).
• Fixed the OWLViz Tab, which was broken in build 500.
• Fixed the OWL Wizards, which were also broken in build 500.
• Fixed a problem with the file browser for local folder repositories.
• Added a getHasValues(RDFProperty) method to the OWLNamedClass interface.
• Fixed a problem with getHasValuesOnTypes method in the RDFIndividual interface.

IMPORTANT: This build is a major change from the previous build and is likely to have some initial glitches due to the introduction of so much new functionality. Please save your work before trying this build, don't use it for mission critical applications, etc.

The motivation for such major change are three significant improvements to Protégé that users have been requesting for a long time:

• Database inclusion - Until now, database inclusion has not been available in Protégé. This has led to many workarounds and inconveniences for users who want to work with ontologies in database mode. For users who are ready to try out this functionality, we have written a web page describing how to use the database inclusion mechanism. Please note that there has been an incompatible change in the database format and you will not be able to use existing database projects. You will need to use build 130 or prior to convert your project to a file-based format and then use the new build to convert the file-based project back into a database project.
• New Protégé-OWL parser - The previous version of the Protégé-OWL parser had many problems that made it fragile, perform badly, and use lots of memory. The new parser is much more robust, uses significantly less memory, is much faster, and has better support for untyped resources.
• Decoupled namespace management - There have been many complaints about the way Protégé handles namespaces. For example, users have requested better URN support and a decoupling of the name of the xml:base, ontology name, and the default namespace. In previous versions of Protégé, the namespace code was tightly coupled with the underlying OWLModel, which led to many quirks in the way Protégé behaved. Now the namespace management code is a thin layer which defines how the ontology is presented to the user. This build provides better URN support and better xml:base, ontology name, and default namespaces decoupling.

Known Limitations - ( please read! )

1. The database schema used by the database back-end has changed in an incompatible way. This means that to use an existing database project with the new build, you will first have to convert it to a file-based project (in build 130 or prior) using the File | Convert Project to Format... menu item. Then, open the file-based project with the new build and convert it back to database format.
2. For OWL projects, the format of the PPRJ file (.pprj) has changed in an incompatible way. The new version of Protégé will be able to read existing PPRJ files, but when these files are saved they will not be properly understood by previous versions of Protégé.
3. Another important change is that the internal names of the ontology entities are now the fully qualified name, rather than the prefixed name, which may impact application developers. We recommended that developers adapt your code to use full names. The short name is still supported, but may have a performance impact. The support for short names can be disabled, by setting the owlmodel.expand.short.name.in.methods property in the protege.properties file to false. The class edu.stanford.smi.protegex.owl.model.NamespaceUtil provides conversion methods between the full and short names of ontology entities. If you are developing a user interface, we recommended that you display the browser text of an entity, which shows the prefixed name.
4. Although we tried to test as many plug-ins as possible, some plug-ins may need to be adapted to this new build. If you notice any plug-ins misbehaving, please report them on the appropriate Protégé mailing list.
5. If you have existing Collaborative Protégé projects in OWL, you will not see the annotations attached to the ontology components anymore, because the name of the entities in the annotation ontology used to be the short name, rather than the long name. Shortly, we will provide a conversion routine that will adapt existing annotation projects to use the full name of entities.

Changes in Bundled Plugins

• Upgraded to version 1.3 of the DataMaster plug-in, which contains some major bug fixes and improvements. Please see the DataMaster 1.3 wiki page for more details.

General

• 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 Protege.

Changes in Protégé-OWL

• The display of inferred types in the Individuals tab can be now configured to a) show all types (default), or b) show direct types only. Instructions for configuring the second option are available on our Wiki.
• There is a new option available for code generation to include prefixes in the generated Java names. This option is configurable via Code | Generate Protege-OWL Java Code... | Include prefixes in generated Java names.

Changes & Bug Fixes in Protégé-OWL

• Fixed a bug for the conversion of owl:differentFrom in the implementation of the direct Pellet reasoner that caused an error message to be displayed at reasoning time: "Error at synchronization:edu.stanford.smi.protegex.owl.model.DefaultOWLAllDifferent".
• Removed a warning from the console when using the triples view for individuals.
• Fixed a bug in the OWLDateWidget that was preventing users from being able to change the value of the date.

Changes in Core Protégé

• Archive and Revert functionality now works for database projects. "Archive" will create a copy of the current version of the ontology in a new database table. "Revert" will override the current table with the contents of a previously versioned table. (Please note: this is not yet working for PostgreSQL - we are working on a fix for this).
• The list of display slots in the Forms tab is now sorted alphabetically.

Changes & Bug Fixes in Protégé-OWL

• Fixed a bug for the conversion of owl:differentFrom in the implementation of the direct Pellet reasoner.
• Fixed a bug that caused type information to be lost for some inferred data property values.
• Upgraded to Jena 2.5.4

Changes in Collaborative Protégé

• The search results panel on the Search tab now contains an additional button to show the annotated entity from the user ontology.

Changes in HTML Chat (also part of Collaborative Protégé)

• The ChatTab plug-in now supports text in HTML format (Bold, Italics, Underline, Strikethrough). Hyperlinks to Web pages can be followed by clicking on them in the chat window.
• Users are able to reference (in a chat message) an internal entity from the ontology by using the syntax @'EntityName' (e.g., @'Pizza'). Clicking on the internal link will bring up a window showing the ontology entity.
• The ChatTab now displays a list of the users that are online.

Additional documentation and a user's guide is available on our Wiki.



Changes & Bug Fixes in Core Protégé, Standard Extensions

• Added support in the client-server version of Protégé for loading projects from HTTP addresses.
• Fixed a bug in the graph widget that was causing nodes to be drawn behind the palette when users added exisiting instances to the graph.

Changes & Bug Fixes in Protégé-OWL

• Added a getIndividualDirectTypes method to the reasoning interface (ProtegeReasoner) for getting the direct inferred types of an individual.
• Bug fix for "Compute inferred types" for the Pellet implementation of the direct reasoner (available in the GUI via the context menu) to return all the types of an individual rather than just the direct types.
• Bug fix for the DIG rendering of owl:AllDifferentFrom.
• Bug fix for the getURIForResourceName method of the OWLModel interface for client-server mode.

Changes & Bug Fixes in Protégé-OWL

• Modified the SWRLTab and the SWRL Jess Bridge to support inference over larger ontologies.
• Added additional operators to the temporal built-in library.
• SWRL system classes are now hidden from the user interface by default.
• Made some performance improvements for ontology entities creation for large ontologies.

Changes in Standard Extensions

• Fixed a bug with complex links in the graph widget that was only occurring in Protégé's client-server mode. The first time users drew a complex link between two nodes, the link disappeared, and only reappeared after clicking away from the graph and coming back.
• Fixed two bugs in the graph widget that were only occurring with graphs from included projects:
  • The graph widget's "Remove Selected Instances" button is no longer enabled on graphs from included projects.
  • Users are no longer able to create new nodes and links on graphs from included projects.

Changes & Bug Fixes in Core Protégé, Protégé-Frames

• A full API for accessing information in the Metaproject, which is used to configure the Protégé server, is now available in the edu.stanford.smi.protege.server.metaproject package.
• Two new slot widgets called "EditorPane" and "EditorPanePlain" have been added to the standard distribution. These widgets allow rendering and editing of slot values as HTML text, which facilitates the inclusion of links as part of a slot value. Documentation is available on the Wiki:
  
  http://protegewiki.stanford.edu/index.php/EditorPanePlain
  http://protegewiki.stanford.edu/index.php/EditorPane
  
  
• Added support in Protégé's client-server mode for included forms and browser text for Frames projects. The forms for included projects are now also visible in the including project. This was a limitation in previous versions of Protégé.
• The position information for nodes in the graph widget that is stored in included projects is now available in including projects. This was a limitation in previous versions of Protégé.

Changes & Bug Fixes in Protégé-OWL

• Fixed a bug in the integrated reasoner that caused some consistent ontologies to be reported as inconsistent. The current version does not provide support for reasoning with SWRL rules.
• Added support for searching of OWL entities using synonym properties, which can be any annotation property that takes a literal as a value. Configuration for the search synonym properties is accessible in the OWL menu under Preferences -> Searching.
• Fixed the display of symmetric, transitive, and inverse functional properties that do not have owl:ObjectProperty as a declared type.
• Added support in the native writer for SWRL rules.

Changes in DataMaster

• Version 1.2.1 of DataMaster fixes a bug caused by calling jumping methods (like last(), beforeFirst(), etc.) on FORWARD_ONLY ResultSets returned by some databases (like Oracle) when queried for primary keys. This version also contains some improvements for more general JDBC driver compatibility.

This build contains an important change to the Protégé-OWL editor, which is the ability to connect directly to the Pellet reasoner. Previously, Protégé-OWL only supported connections to an external DIG reasoner. This change includes modifications to the user interface and the Protégé-OWL API, which are detailed in the following two sections:

UI Changes

• Reasoning functionality is now accessible through the new "Reasoning" menu, which allows users to select from a list of available reasoners. The current choices in this menu are "DIG Reasoner" and "Pellet 1.5.1 (direct)". All reasoning actions such as consistency checking, classification, etc., will work with the selected reasoner.
• It is now possible to query the inferred property values of an individual. This can be done by right-clicking on an individual in the Individuals tab and selecting "Get inferred property values" from the context menu.

API Changes

• The old ProtegeOWLReasoner reasoner interface has been deprecated and the new ProtegeReasoner interface should be used instead. Documentation for accessing the reasoner programmatically using the new interface is available on the Wiki.
• A new plug-in type called a "Reasoner Plug-in" has been introduced that allows developers to plug other reasoners into Protégé-OWL. Currently, there are four implementations of the reasoner plug-in: 1) Jena reasoner, 2) DIG reasoner, 3) Pellet reasoner accessed through the Jena API, and 4) Pellet reasoner accessed through the OWL-API. We have made the DIG reasoner and the Pellet reasoner accessed through OWL-API available through the user interface via the Reasoning menu. Documentation for developing a reasoner plug-in is available on the Wiki.
• The protege-pellet.jar file in the edu.stanford.smi.protegex.owl.inference.pellet folder contains a programmatically accessible Protégé-OWL to OWL-API converter. This allows developers to obtain an OWL-API model from a Protégé-OWL model. The model is a snapshot and not a synchronized (live) copy and the limitations of the conversions are documented in the Javadoc for OWLAPIConverter. We would like to thank clark&parsia for providing an important part of the converter code.

Please note: when using the direct Pellet reasoner with large ontologies, we recommend that users increase the allocation for Protégé-OWL's heap size because Protégé-OWL and Pellet will share the same memory space. In the event that you get an OutOfMemory exception during reasoning, Protégé-OWL will try to recover, but we do not recommend that you try to save your file after this type of exception.

Other Changes

Protégé-OWL users who use rdf:label to represent class names now have the ability to put spaces and other characters in class names. In the past, the restriction editor was not very friendly to such users because it could not parse expressions such as "hasTopping some My Favorite Type of Topping". We have modified the grammars used by the restriction editors so that names with spaces can be quoted. For example, the expression above can be represented as "hasTopping some 'My Favorite Type of Topping'".



Changes & Bug Fixes in Protégé-OWL

• Ontologies with SWRL rules no longer need to explicitly import swrl.owl and swrlb.owl, so the use of SWRLTab-generated OWL files with other tools and reasoners should be easier
• Fixed a bug in sqwrl:count built-in, which caused it to produce inconsistent counts.
• Extended and fixed some bugs in the SWRL mathematical expressions built-in library.
• Improved performance of the SWRL editor when it is used with large ontologies
• Implemented negative operators in the SWRLTab temporal built-in library.
• Fixed a bug that prevented users from adding an owl:equivalentProperty to another property in the Protégé-OWL user interface. This can now be done in the Properties Tab:
  • switch the Annotations table to the triples view
  • click on the "Add existing resource as value" icon
  • select the owl:equivalentProperty property
• The PropertiesTab now comes up correctly even if an ontology contains properties that are both datatype and object properties (making the ontology OWL Full). This limitation previously effected the display of properties of the FOAF vocabulary.

Changes in Collaborative Protégé

• Users can now configure which collaborative tabs (annotations, changes, chat, search, etc.) they would like to have displayed. Configuration is accessible from the Collaboration | Configure menu item. See the documentation section on Collaborative Protégé for more information: http://protege.stanford.edu/doc/collab-protege/index.html#Configure.

Changes in Standard Extensions

• Fixed a bug in the graph widget. When nodes were removed rather than deleted from the graph, the slot that users designated to hold transitions was not being updated.

Changes & Bug Fixes in Protégé-OWL

• Updated the query built-ins to SQWRL Built-In Library. This update requires that ontologies using the existing SWRL query library must change the prefix of their query built-ins from 'query' to 'sqwrl' when they upgrade to the latest beta. The operation of the built-ins in the new library is identical to the superseded library. However, the new library has a number of new built-ins that expand the power of queries and more will be added over the next few months.
• Added a new XML Query Built-In Library. SQWRL queries can now work directly on XML documents.
• Added a new Mathematical Expression Parser Built-In Library. This library allows complex mathematical expressions to be used in SWRL rules or SQWRL queries.
• Updated the SWRL Built-In Bridge API. This will require a very minor change to existing libraries implemented using this bridge: Java built-in implementations now take a list of BuiltInArgument rather than Argument objects.
• Fixed a problem that caused some widgets in the Individuals tab to be disabled. Users were not able to add new values to properties attached to individuals.
• In the Individuals tab, searches are now performed using the browser text of the individuals.

Changes & Bug Fixes in Core Protégé, Protégé-Frames

• Made two changes that improved the performance of the Instances tab:
  • Added the ability to disable the display of instance counts in the Class Hierarchy pane. Normally, Protégé displays the number of instances for each class in the class hierarchy in parenthesis next to the class name. This was causing problems when users clicked on a class with thousands of subclasses because calculating the number of instances for each of the subclasses was taking too much time. To disable the display of instance counts, go to Project | Configure... | Options and check the box next to "Suppress Instance Count Display".
  • The pane in the Instance Browser that displays instances of a particular class is now multithreaded. If a user selects a class that has thousands of instances, viewing those instances in the Instance Browser is much faster.
• Users can now pass arguments to Protégé's main method in the form of -propMyProp=MyValue, where -prop is the prefix for all property-value assignments. These properties are accessible in the same way as properties from the protege.properties file.
• Added some utility methods in SystemUtilities for getting system properties.
• When exporting a Protégé-Frames project to OWL, users now have the option of choosing the native OWL writer rather than the default Jena writer. Please note that there is a known limitation if using the native writer: Protégé-Frames projects that contain PAL constraints are not exported correctly. If your project has PAL constraints, please continue to use the default writer.

Changes & Bug Fixes in Protégé-OWL

• The Protégé-OWL Java Code Generator now generates getXXXProperty methods on Factory classes.
• Added a method in the OWLModel interface for creating simple annotation properties.
• Added support in the Properties tab user interface for creating simple annotation properties.
• Fixed a bug related to saving the inferred hierarchy.
• Filtered out the SWRL and SWRLB entities from the DIG translation, which caused some reasoners to report warnings or errors.
• Made the Help menu more user friendly:
  • Combined the "About Protégé..." and "Protégé-OWL Version Info..." menu items into one item called "About Protégé-OWL...". The dialog that results from choosing this menu item no longer has any Protégé-Frames specific text, such as the link to the protege-discussion mailing list.
  • Added an item that links to the "Getting Started with Protégé-OWL" page on the Protégé website.
  • Added an item that links to the Protégé-OWL FAQ page on the Protégé website.
• Implemented a fix for DIG's translation of boolean properties. Thanks go to Thomas Russ for suggesting the fix.
• Several minor bug fixes in Protégé-OWL's SWRL support.