WebProtegeReleaseNotes

WebProtege Release Notes

WebProtege 0.5 Beta Series

Beta Build 500 - May 13, 2011

• Compatible with Protege 3.4.6 (for the external server mode), GWT 2.2.0, Java 1.6

New functionality

• Restriction editing is supported in the Restriction Portlet. The portlet has support for auto-complete for entity names.

• Threaded notes and discussions are now supported in he Notes Tree Portlet.

• The Properties View Portlet shows the properties that are in the domain of the selected class, similar to the Properties View in Protege 3.x.

• WebProtege now enforces the read and write access right permissions as defined in the metaproject.

• Users can now sign in with their OpenID account, such as Google, Yahoo, AOL, Flickr, etc. The first time a user signs in with the OpenID, she will be prompted to associate it with a WebProtege account. For subsequent sign ins, the user can simply use the OpenId. The associated OpenId accounts can be edited in the Options menu -> Edit profile.

• It is now possible to watch a class or a branch in the class tree, similar to the Watch functionality available in wikis. The Watched Entities portlet will display the changes that occurred in the watched entities and branches.

• The users may opt to be notified of changes occurring in their watched entities or branches, as well as in the notes and discussions attached to these entities. The notification is sent by email and can be configured, together with the notification frequency, in the Options menu -> Edit profile.

• It is now possible to create direct links to entities in the ontology that will open WebProtege with the entity selected. The direct link to a class in the ontology can be retrieved by right clicking on the class in the class tree and selecting Show direct link from the context menu. This link can then be sent by email or instance messaging to other users.

• Users may now change their password from the Options -> Change password menu in the top right corner of the display. The password can be reset and sent by email if the user clicks on the Forgot password link in the Login panel.

• Users with adequate access rights can create new users from the Options menu -> Add new user.

• It is now possible to close the access to a WebProtege installation by requiring a password to get to the initial page of an ontology.

UI Layout Enhancements

• WebProtege stores the user interface configuration in a XML file that can be manually edited to change the layout of tabs and portlets.

• Added support for building domain specific knowledge acquisition forms. Forms are similar to the ones in the Protege 3.x series in which a property in the ontology is associated to a widget that can display and edit the values of the property. Available property widgets: text field, text area, combo box, grid, etc. See documentation.

• New property form widgets:
  • Instance check box
  • Instance radio button
  • Instance combo-box
  • Class select widget
  • Property select widget

• It is now possible to create your own tabs, add portlets to them, and set a controlling portlet for the tab. The controlling portlet sets the selection for the rest of the portlets in a tab. For example, in the Classes tab, the class tree portlet is the controlling portlet.

• It is possible to change the controlling portlet of an existing or new tab dynamically at run time by using the configure icon in the title bar of a portlet.

• The selection in the different tabs is now synchronized. For example, if a user selects a class in the Classes tab, and then switches to the Individuals tab, the same class will be selected.

• You may save the layout from the Ontology toolbar using the Save icon (right-most icon). This feature is still under development.

• It is now possible to set the order of a portlet in a tab in the configuration xml by using the <index> element.

Other enhancements and bug fixes

• Better support for linking terms from BioPortal ontologies with the BioPortal Reference Portlet:
  • Added support for composite search: each search term will be expanded
  • Added support for searching on synonyms and on other property values
  • The search results presentation has been enhanced. It shows the preferred term, show whether the search term was found in preferred term, synonym or id, and the matched content.

• The Parents Portlet displays the direct superclasses of the selected class with clickable links for easy navigation.

• Fixed the All Properties Portlet that shows the annotations (or own slots for Frames ontologies) associated to an entity in the ontology. The language of a rdfs:literal is now also editable.

• Fixed a resizing issue for the top panel of WebProtege.

• The properties stored in the protege.properties are now available to both the client (UI) and the WebProtege server. Properties that are not supposed to be shared with the client can be black-listed in a file blacklist.properties.

• Updated developer documentation on setting up WebProtege in Eclipse.

WebProtege 0.5 Alpha Series

Build 300 - August 15, 2009

• Various fixes and enhancements

Build 200 - August 15, 2009

Critical Changes (please read)

• Upgraded to GWT 1.7.
• We made some changes to the directory structure and Eclipse setup to conform to GWT 1.7. If you are installing WebProtege, please re-read the Administrator's Guide for updated instructions. Developers should look at the Developer's Guide - the setup for compiling and running WebProtege has been greatly simplified thanks to the Google Plugin for Eclipse.
• WebProtege now runs in "local mode" by default. Local mode means that WebProtege will load ontologies from a standalone instance of Protege in your Servlet container. WebProtege can also be configured to run in "external server mode" by setting a property value in the protege.properties file in the <your-servlet-container>/webprotege directory. External server mode means that WebProtege will load ontologies from a Protege server running outside of your Servlet container. The following additional configurations options can be set in protege.properties:

  # Defaults to false; change to true to run WebProtege in external server mode
  load.ontologies.from.protege.server=true
  
  # Use to specify an alternative location for the metaproject if running in local mode
  local.metaproject.path=/tmp/metaproject.pprj
  
  # Hostname of the Protege server if WebProtege is running in external server mode; can also contain a port number
  server.hostname=localhost
  
  # Username that WebProtege uses to connect to the Protege server if running in external server mode
  webprotege.user=webprotege
  
  # Password that WebProtege uses to connect to the Protege server if running in external server mode
  webprotege.password=webprotege
  
  # Automatic save interval for ontologies if running in local mode (we recommend the database back-end instead of file mode)
  server.save.interval.sec=120
  

  Values of properties listed above should be changed to match your custom WebProtege installation.

• Project configurations are now saved in the <your-servlet-container>/webprotege/projectConfigurations folder. The XML configuration files contain user interface layout information (tabs to display, number of columns in a tab, portlets to display in a tab, portlet properties, etc.). The default configuration file is "configuration.xml". New configuration files are automatically generated if a user saves the layout for a particular project. Configurations are stored per user, per project.
• Users can now open multiple ontologies in WebProtege. Each ontology is displayed in a separate tab.

Other Changes

• Search is now implemented, including the ability to jump to the location in the class tree of a selected search result (this functionality is not yet available for the properties tree). The search text field is located in the top toolbar.
• Added more support for editing; users with write permission on a particular project are now able to:
  • Create and delete classes in the Classes tab
  • Create and delete properties in the Properties tab
  • Edit string property values in the Properties portlet
  • Edit the domain and range of properties in the Properties tab
• New portlet is available; the BioPortal Search portlet allows users to search for terms in the BioPortal repository and import the terms as references in WebProtege ontologies.
• New portlet is available; the PropertyFieldPortlet allows form-based editing of property values. The portlet can be configured to use different widget types for different properties (analogous to slot widgets in Protege standalone). Available widgets for editing include:
  
  
  • textfield
  • textarea
  • HTML pane
  • instance grid (similar to the InstanceTable in Protege standalone)
  • external reference
  • multifield
  • combo-box; not working yet... :)
  .
  The layout of the form has to be done manually (for now) in the XML configuration file. An example is available in the "configuration_example_property_field_portlet.xml" included in the standard distribution.
• The Properties tab now shows different icons for the different property types.
• The Class Tree in the ClassTreePortlet can now be configured to only show a subtree in the ontology. The root class can be configured in the configuration XML file of the project, by setting the topClass portlet property to the full name of a class. Please see the example configuration file for exact syntax: "configuration_example_property_field_portlet.xml".
• Web links are now opened in a new browser window.
• Better logging in the Servlet container and Protege server logs if something goes wrong.
• If running in external server mode, WebProtege will cleanly handle situations in which the Protege server becomes unavailable.
• RPC calls are now available for creating/deleting classes and setting property values.
• Support for multiple change events. Portlets can register listeners for class and property creation, deletion, and for property value changed.

Build 103 - August 1, 2009

If running in external server mode, WebProtege is now compatible with the Protege 3.4.1 release.

Build 102 - April 3, 2009

If running in external server mode, WebProtege is now compatible with the Protege 3.4 release.

Build 101 - October 26, 2008

Initial 0.5 alpha release