WebProtegeReleaseNotes

WebProtege Release Notes

We have migrated all WebProtege releases and release notes following build 105 to GitHub. For all new releases, please use the WebProtege GitHub page to access the release notes.

Go back to the WebProtege main page.

WebProtege Build 105 (July 24, 2013)

New portlets:

• Usage portlet - shows the usage for the selected class, property or individual. Usage can be filtered by type of entity, axiom etc. and can be sorted by entity, entity type, axiom type etc.
• Ontology Id portlet - displays the id of the project root ontology (currently read only)
• Ontology Annotations - displays the annotations for the project root ontology

Bug Fixes:

• Some application properties were ignored e.g. Application Name -- Fixed
• Several fixes of the Property Form Portlet:
  • The Property Grid widget didn't work at all -- Fixed
  • Simple property widgets would display strange values after editing -- Fixed
• Changed the size of portlets in the default layout (people with local installations who want these changes will need to delete the existing default configuration files so that the new ones are copied over on start up).

Enhancements:

• Some cosmetic UI enhancements e.g. progress bars and message boxes now use native gwt widgets

WebProtege Build 104 (July 5, 2013)

User Interface:

• Fixed a design issue with the properties portlet which caused annotations not to be displayed.
• Made the properties porlet display superclasses that are SomeValuesFrom and HasValue restrictions as property values.

OBO:

• WebProtege now uses the "reference" OBO Format parser for parsing OBO ontologies.
• Improved the layout and utility of the various OBO metadata editing widgets.

Other:

• Fixed a bug that caused the link in watch notification emails to be incorrect.
• Turned off recaptcha verification from sign up dialog.

WebProtege Build 103 (May 20, 2013)

• Fixed a problem that caused the class hierarchy stop expanding in some cases
• Changed the presentation of notes so that note status (resolved or unresolved) is shown on a new line

WebProtege Build 102 (May 15, 2013)

• WARNING (if you have a local installation of WebProtege): We have renamed one of the portlets, which affects the default configurations of the projects. Please delete the default-ui-configuration-data from your WebProtege data directory, and then restart tomcat. WebProtege will copy the new default configurations back to that folder.

• Fixed problem related to watches not being persisted in some cases

WebProtege Build 101 (May 2, 2013)

• Fixed problem related to downloading of ontologies from Firefox

MAJOR NEW WebProtege Release (Build 100, April 25, 2013)

We are pleased to announce the availability of a new version of WebProtege at http://webprotege.stanford.edu. This release constitutes a major new release with many new features and improvements.

Please, try it out and let us know what you think!

Read below about some of the more exciting features:

Sharing:

• "Google docs" style mode of operation - upload and share ontologies with colleagues and collaborators.
• Access control - ontologies can be public or private with controlled lists of users who can read, write and comment.
• Discussion support - discussion threads for entities make it easy to add issues, todo notes and queries.

User Interface:

• Simplified user interface - for editing lightweight OWL ontologies (our default configuration for OWL ontologies makes them much easier to edit for both non-experts and experts)
• Editing assistance - autocompletion for class, property and individual names
• Fast editing - on-the-fly creation of properties, classes and individuals (you not longer need to define classes and properties upfront before using them)
• Bulk creation - quickly sketch out class and property hierarchies using bulk entry for subclasses and subproperties
• OBO support - import OBO ontologies and use forms designed for editing OBO constructs and metadata

OWL 2 support:

This release uses the OWL API and supports editing of lightweight OWL 2 ontologies natively.

Change Tracking:

• Full change-history logging - inspect changes by change type, timestamp, author etc.
• Revision tracking - download any revision of an ontology at any time.

We strongly encourage you to use the online version of WebProtege at http://webprotege.stanford.edu. We provide regular data backup, maintenance and updates for this version. However, this release is also available for download and local installation.

Finally, we recommend that existing users of Webprotege 1.0 (now hosted at http://wp-obs.stanford.edu) download and move their ontologies to this new version. While the previous version will continue to be hosted, all future development such as new features and bug fixes will take place on the new version.

WebProtege 1.0 Final Release (April 25, 2013)

We are happy to announce the WebProtege 1.0 release that will be our last release of WebProtege, which is using the Protege 3.x backend.

We have been working very hard on a new generation of WebProtege that has a new and simplified user interface and provides many new exciting features. This new generation of WebProtege is based on the OWL-API and fully supports OWL 2.0. Please stay tuned for the announcement of the new WebProtege, which will come very shortly. The rest of the email refers to the WebProtege 1.0 release.

There are a few important announcements related to the WebProtege 1.0 release:

• The WebProtege 1.0 demo server has been moved from http://webprotege.stanford.edu to http://wp-obs.stanford.edu

• If you have ontologies hosted on the WebProtege 1.0 server, please follow the instructions for moving them to the upcoming WebProtege server, which will be hosted at http://webprotege.stanford.edu. While we plan to maintain for a while the WebProtege 1.0 server, we strongly encourage you to move your ontologies to the new server. We are happy to answer any questions and help you with the ontology move. Don't hesitate to contact us.

• If you are accessing the ontologies from the Protege 3.x desktop client, please use the new host name: wp-obs.stanford.edu:5200 when connecting to the Protege server.

Enhancements and Fixes in WebProtege 1.0

• A download link is now available in the MyWebProtege tab that allows users to download the latest snapshot of an ontology. The download is supported for OWL ontologies only. If you want to download other ontology formats (e.g. RDF or Frames), please contact us and we are happy to assist you.

• It is now possible to use as login name your email address that is associated to your WebProtege profile (You can see the email address in the Options menu -> Edit profile -> Email).

• The AllPropertiesPortlet also includes now the rdfs:seeAlso and rdfs:isDefinedBy in the list of properties that can be edited for an entity.

• It is now possible to create different forms for individuals based on their types by using the 'types_any' property in PropertyFormPortlet. Limitation: the forms are currently not inherited to subclasses.

• Double-clicking on a row in the Changes portlet will bring up a new window with the details on the change.

Download and Install

The download and install instructions are available in the WebProtege 1.0 Administrator's Guide.

WebProtege Beta Series

February 7, 2013

Take a look at the recorded NCBO webinar on publishing and editing OWL2 and OBO ontologies with WebProtege 2.

We are very excited to announce WebProtege 2.0 Beta!

Please navigate to http://webprotege-beta.stanford.edu/ to try it out. Let us know what you think via the WebProtege mailing list: https://mailman.stanford.edu/mailman/listinfo/webprotege-feedback.

Key new features:

• WebProtege now supports OWL 2 ontologies, thus allowing users to take full advantage of WebProtege's collaboration capabilities to develop OWL 2 ontologies in a distributed way.

• Users can now upload OBO Format ontologies and edit them collaboratively. When a user opens an OBO Format ontology, the user interface is custom-tailored with a set of OBO-specific widgets that makes it easier to edit OBO term metadata (see attached screenshots). All of WebProtege's collaboration capabilities are available for use with OBO Format ontologies.

• WebProtege now has a content management system. Users can log in and upload their ontologies to the server, edit them, invite collaborators to contribute, and set permissions for collaborators (who can then view, edit, or make comments).

January 12, 2013

Screenshot of OBO-specific widgets - new in 2.0 beta!

We are very excited to announce WebProtege 2.0 beta! We're looking for feedback on this new version of WebProtege, currently available for use on our demo servers here at Stanford:

http://webprotege-beta.stanford.edu/

Release Highlights

This section describes changes relative to WebProtege 0.5

• WebProtege now supports OWL 2 ontologies, thus allowing users to take full advantage of WebProtege's collaboration capabilities to develop OWL 2 ontologies in a distributed way.
• Users can now upload OBO Format ontologies and edit them collaboratively. When a user opens an OBO Format ontology, the user interface is custom-tailored with a set of OBO-specific widgets that makes it easier to edit OBO term metadata. All of WebProtege's collaboration capabilities are available for use with OBO Format ontologies.
• WebProtege now has a content management system. Users can log in and upload their ontologies to the server, edit them, invite collaborators to contribute, and set permissions for collaborators (who can then view, edit, or make comments).

June 4, 2012

• Initial software release to demo server http://webprotege-beta.stanford.edu/.

WebProtege 0.5 Beta Series

Beta Build 501 - May 28, 2011

• The All Properties Portlet (used to show the annotation properties and other properties attached to entities) supports now the editing of instance values.

• Fixes for the editing of String values in the All Properties Portlet

• Provided utility methods in the edu.stanford.bmir.protege.web.client.ui.util.SelectionUtil class for the selection of classes and individuals in the ontology.

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 the Notes Tree Portlet.

• The HTML Message Portlet allows the embedding of arbitrary HTML pages or snippets as part of a WebProtege tab. This portlet can be used for warnings, alerts, news, embedded documentation, and so on.

• 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 restrict 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. The configuration can be generic (applied to all projects), project specific (applied to one project for all users), or project/user specific (is custom for a project and user).

• 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

• Several of the property form widgets can be configured to work with single or multiple cardinality properties by setting the flag multiple_values_allowed to true/false in the XML configuration for the portlet.

• It is possible to prevent users from changing the layout of their WebProtege by hiding the Ontology toolbar in the XML configuration file by setting the flag showOntologyToolbar to false in the <project> element. It is also possible to prevent users from closing a tab by setting the closable flag to false in the tab XML configuration.

• The Properties Form Portlet supports now type-based tab activation. The tabs in the portlet can be configured to show up only if the selected entity has certain types (e.g. rdf:type).

• 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 search can be restricted to a subset of BioPortal ontologies

• 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.

• Various other bug fixes and enhancements

• Updated developer documentation on setting up WebProtege in Eclipse.

WebProtege 0.5 Alpha Series

Build 300 - May 12, 2010

• 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 bioontology.org/tools/portal/bioportal.html 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