[protege-releases] Protege 3.5 Release

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We are pleased to announce that Protege 3.5 has moved from beta to 
release status.

Download link for registered users:

http://protege.stanford.edu/download/registered.html#p3.5

New users, please register before downloading:

http://protege.stanford.edu/download/register.html

A detailed release announcement with important installation notes is 
available on the Protege wiki:

http://protegewiki.stanford.edu/wiki/Protege_3.5_Release_Notes


Release Notes
----------------------

*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*
- The Protege native writer export is now done in a more efficient way 
on the server, when running in client-server mode. 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 <http://protege.cim3.net/cgi-bin/wiki.pl?SWRLTab> now 
supports the Drools rule engine <http://www.jboss.org/drools>. A new tab 
called the SWRLDroolsTab 
<http://protege.cim3.net/cgi-bin/wiki.pl?SWRLDroolsTab> provides a 
graphical interface for interacting with this implementation. The 
existing SWRLJessTab 
<http://protege.cim3.net/cgi-bin/wiki.pl?SWRLJessTab> is still 
available. All existing SWRL built-in libraries 
<http://protege.cim3.net/cgi-bin/wiki.pl?SWRLTabBuiltInLibraries> are 
supported in the Drools implementation. Both the Drools and Jess 
implementations now use a pair of OWL 2 RL 
<http://www.w3.org/TR/owl2-profiles/#OWL_2_RL>-based reasoners for 
performing inference (read more 
<http://protege.cim3.net/cgi-bin/wiki.pl?SWRLTabOWL2RL>). These 
reasoners are also used by the SQWRL 
<http://protege.cim3.net/cgi-bin/wiki.pl?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 <http://protege.cim3.net/cgi-bin/wiki.pl?SWRLTabAPIUpdating>. 
The process of building the SWRLTab and its associated rule engines has 
also changed. The new build process is outlined here 
<http://protege.cim3.net/cgi-bin/wiki.pl?SWRLTabBuilding>.

*BioPortal Import Plug-in*
Made significant enhancements to the BioPortal Import Plug-in 
<http://protegewiki.stanford.edu/wiki/BioPortal_Import_Plugin>:

- 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 
<http://protegewiki.stanford.edu/wiki/Collaborative_Protege>.

*Change Management*
Added Java utilities for exporting changes and notes as CSV files. 
Source code 
<http://smi-protege.stanford.edu/repos/protege/change-management/trunk/changesUtil/> 
and export scripts 
<http://smi-protege.stanford.edu/repos/protege/change-management/trunk/scripts/> 
are available in our Subversion repository.

Please post questions and feedback to the Protege 3.x support mailing 
list <https://mailman.stanford.edu/mailman/listinfo/protege-owl>.

Best Regards,
The Protege Team


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<html>
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    <meta http-equiv="content-type" content="text/html; charset=ISO-8859-1">
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  <body bgcolor="#FFFFFF" text="#000000">
    We are pleased to announce that Protege 3.5 has moved from beta to
    release status.<br>
    <br>
    Download link for registered users:<br>
    <br>
    <a href="http://protege.stanford.edu/download/registered.html#p3.5">http://protege.stanford.edu/download/registered.html#p3.5</a><br>
    <br>
    New users, please register before downloading:<br>
    <br>
    <a class="moz-txt-link-freetext" href="http://protege.stanford.edu/download/register.html">http://protege.stanford.edu/download/register.html</a><br>
    <br>
    A detailed release announcement with important installation notes is
    available on the Protege wiki:<br>
    <br>
    <a
      href="http://protegewiki.stanford.edu/wiki/Protege_3.5_Release_Notes">http://protegewiki.stanford.edu/wiki/Protege_3.5_Release_Notes</a><br>
    <br>
    <br>
    Release Notes<br>
    ----------------------<br>
    <br>
    <b>Core Protege</b><br>
    - Dialogs are now centered in the main window.<br>
    - System slots can now be selected for export to CSV in the Query
    Tab.<br>
    - Fixed a bug that prevented the Finish button from being enabled
    when creating a database project.<br>
    <br>
    <b>Protege-OWL</b><br>
    - The Protege native writer export is now done in a more efficient
    way on the server, when running in client-server mode. The
    performance increase should be significant, especially on slow
    networks.<br>
    - Fixed a bug in the Protege native writer that prevented some
    untyped resources from being exported.<br>
    <br>
    <b>SWRL</b><br>
    The <a href="http://protege.cim3.net/cgi-bin/wiki.pl?SWRLTab">SWRLTab</a>
    now supports the <a href="http://www.jboss.org/drools">Drools rule
      engine</a>. A new tab called the <a
      href="http://protege.cim3.net/cgi-bin/wiki.pl?SWRLDroolsTab">SWRLDroolsTab</a>
    provides a graphical interface for interacting with this
    implementation. The existing <a
      href="http://protege.cim3.net/cgi-bin/wiki.pl?SWRLJessTab">SWRLJessTab</a>
    is still available. All existing <a
      href="http://protege.cim3.net/cgi-bin/wiki.pl?SWRLTabBuiltInLibraries">SWRL
      built-in libraries</a> are supported in the Drools implementation.
    Both the Drools and Jess implementations now use a pair of <a
      href="http://www.w3.org/TR/owl2-profiles/#OWL_2_RL">OWL 2 RL</a>-based
    reasoners for performing inference (<a
      href="http://protege.cim3.net/cgi-bin/wiki.pl?SWRLTabOWL2RL">read
      more</a>). These reasoners are also used by the <a
      href="http://protege.cim3.net/cgi-bin/wiki.pl?SQWRL">SQWRL</a>
    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 <a
      href="http://protege.cim3.net/cgi-bin/wiki.pl?SWRLTabAPIUpdating">here</a>.
    The process of building the SWRLTab and its associated rule engines
    has also changed. The new build process is outlined <a
      href="http://protege.cim3.net/cgi-bin/wiki.pl?SWRLTabBuilding">here</a>.<br>
    <br>
    <b>BioPortal Import Plug-in</b><br>
    Made significant enhancements to the <a
      href="http://protegewiki.stanford.edu/wiki/BioPortal_Import_Plugin">BioPortal
      Import Plug-in</a>:<br>
    <br>
    - Users may now search for terms in all BioPortal ontologies, and
    navigate to a specific BioPortal ontology to import branches of the
    class tree.<br>
    - Added the ability to start multiple import processes at the same
    time.<br>
    - Importing is now done in separate threads, and can be canceled at
    any time by the user.<br>
    - Added a progress dialog to show import progress.<br>
    - 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.<br>
    <br>
    <b>Collaborative Protege</b><br>
    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 <a
      href="http://protegewiki.stanford.edu/wiki/Collaborative_Protege">Collaborative
      Protege</a>.<br>
    <br>
    <b>Change Management</b><br>
    Added Java utilities for exporting changes and notes as CSV files. <a
href="http://smi-protege.stanford.edu/repos/protege/change-management/trunk/changesUtil/">Source
      code</a> and <a
href="http://smi-protege.stanford.edu/repos/protege/change-management/trunk/scripts/">export
      scripts</a> are available in our Subversion repository.<br>
    <br>
    Please post questions and feedback to the <a
      href="https://mailman.stanford.edu/mailman/listinfo/protege-owl">Protege
      3.x support mailing list</a>.<br>
    <br>
    Best Regards,<br>
    The Protege Team<br>
    <br>
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