Difference between revisions of "ProtegeDesktopUserDocs"

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= Protege Desktop User Documentation =
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<span class="orangeBoxTitle">Protege 4.x Documentation</span><br /><br />
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This page contains a collection of links to documentation for end users of the Protege 4.x series.<br /><br />
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This page is the official documentation home for the '''Protege Desktop application versions 4, 5 and higher'''.   
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Protege 4.0 is currently in alpha and we are interested in soliciting your feedback.  We have set up a mailing list specifically for discussion about Protege 4.0.  You can subscribe to the list via the list information page: http://mailman.stanford.edu/mailman/listinfo/p4-feedback.
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</div><br />
 
  
 
__TOC__
 
__TOC__
  
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== General ==
 
  
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=== Protege 4 "to do" list ===
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== Build status & release notes ==
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The latest version of Protege Desktop is '''5.5''':
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* [https://github.com/protegeproject/protege-distribution/releases Release notes]
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* [[Install_Protege5|Installation instructions]]
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* [http://protege.stanford.edu/products.php#desktop-protege Download latest version of Protege]
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You may also download [[Protege_Desktop_Old_Versions|previous versions of Protege]] and read the complete list of release notes. Older Protege 5.0 beta release notes are available [[Protege_5.0_Beta_Release_Notes|here]].
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== Bugs & feature requests ==
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Before you report a bug or feature request, check the [http://protege-project.136.n4.nabble.com/ Protege mailing lists archives] to ensure it hasn't already been reported. If the item is not currently open or you have further information or a question about an existing item, please post a message on the [http://mailman.stanford.edu/mailman/listinfo/protege-user protege-user mailing list].  Give as much detail as possible (including examples or ontologies if possible) as this will help us track things down more quickly.
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Current GitHub issue tracker: https://github.com/protegeproject/protege/issues?state=open
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== Frequently asked questions ==
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We've put together a wiki page to answer the [[Protege-OWL_4_FAQ | most commonly asked questions]] about Protege Desktop.
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== Getting started / tutorials ==
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The Getting started and tutorials have been moved to the [[Main_Page|main page]] of the wiki.
  
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Below is a "to-do" list of things that we are working on integrating into Protege 4.  Please note that these items are not listed in any particular order of priority.  If you have a question about the status of any line item, please post a message on the [http://mailman.stanford.edu/mailman/listinfo/p4-feedback Protege 4 mailing list].
 
  
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* Protege-Frames editor (currently we only have the OWL editor)
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== Editor features ==
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* Protege Web client
 
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* Protege Services
 
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* Client-server support
 
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* Better SWRL support in the Protege-OWL editor
 
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* Better modularization support
 
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* Support for collaborative ontology development
 
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* Forms and browser slot patterns in the Protege-OWL editor
 
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* A database back-end
 
  
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* [[Protege4Features | Overview of features]] - a quick summary of the editor
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* [[Protege4Views | Protege views guide]] - a list of all of the default views that are distributed with Protege
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* [[Protege4Shortcuts | Protege menu guide]] - all of the default menus explained in detail (with keyboard shortcuts)
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* [[Protege4Preferences | Protege preferences guide]] - customizing Protege to your needs
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* [[Protege4NamingAndRendering|Naming and rendering of entities]] - a note on naming things in OWL and configuring Protege to support your naming conventions
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* [[Protege4ExpressionEditor | Protege expression editor]] - adding and editing OWL expressions in Protege
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* [[Manchester_OWL_Syntax|Manchester OWL Syntax]] - an overview of the default syntax used by Protege
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* [[DLQueryTab | DL Query tab]] - how to query using arbitrary class expressions in OWL
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* [[Importing_Ontologies_in_P41|OWL Imports]] -  modular ontology support in OWL and Protege
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* [[Protege4AxiomAnnotations|Axiom annotations]] - how to annotate at axiom level in Protege
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* [[Protege4OWLDiff|Protege OWL Diff]] - compare two versions of an ontology
  
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== User Interface ==
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== Advanced features ==
  
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=== Protege-OWL ===
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* [[BeanShell | The Bean Shell]] - Making complex queries against an ontology.
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* [[Protege4ClientServer | The Protege 4 Server]]
  
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* [[Protege4GettingStarted | Getting started with the Protege-OWL editor]]
 
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* [[Protege4Features | Overview of new features in the Protege-OWL editor]]
 
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* [http://www.co-ode.org/resources/tutorials/protege-owl-tutorial.php A Practical Guide to Building OWL Ontologies using Protege 4 and CO-ODE Tools] (<strong>[[Protege4TutorialErrata|errata page]]</strong>)
 
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* [[Protege4Shortcuts | Menu and keyboard shortcuts]]
 
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* [[DLQueryTab | DL Query tab]]
 
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* [[Manchester_OWL_Syntax|Manchester OWL Syntax]]
 
  
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== Plug-ins ==
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== Further setup / configuration ==
  
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=== Protege-OWL ===
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* [[ChangingTheHeapSize|Adding more memory]]
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* [[EnablingDoubleClick|Double-clicking on OWL files]]
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* [[ClearingP4Preferences|Dealing with Protege preferences problems]]
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* [[Working with firewalls and proxies]]
  
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==== Viewing Plugins ====
 
  
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To see a listing of plug-ins specific to the Protege-OWL editor, go to the Wiki article for the [[Protege-OWL_4.0 | 4.x version of the Protege-OWL editor]].  The list of "Compatible Plugins" on this page is the result of a semantic query that gathers all plug-ins that have declared themselves compatible with the 4.x version of the Protege-OWL editor.
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== Plugins ==
  
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The CO-ODE group at the University of Manchester is the biggest contributor of plug-ins to the Protege-OWL editor.  As such, users may be interested to look at the [http://www.co-ode.org/downloads/protege-x/plugins/ Protege 4 Plugins] page on the CO-ODE Web site, which a listing of only those plug-ins developed at the University of Manchester.  This is a good place to go to download the source code for CO-ODE developed plug-ins.
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=== Finding plug-ins ===
  
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==== Adding Plugins ====
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* Protege will find plugins and updates for you. See our [[EnablePluginAutoUpdate|Auto Update]] page.
  
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If you have developed a plug-in for Protege-OWL 4.0 and you would like to contribute it to the community, follow the following steps:
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* [[Protege-OWL_4.0 | Plugins for Protege]] - the list of all plugins compatible with different versions is available [[Protege_Plugin_Library|here]].
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* Click the [[Special:AddPage/Form:Plugin|New Plugin Link]].  You may want to right click and choose a new window.
 
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* Choose a name for the page  that  discusses the new plugin (e.g. "Sub Ontology Tab").
 
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* Click "Add or Edit"
 
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* Be sure to add  "Protege-OWL" (exactly like so without the quotes) in the Works with field.  Also give the plugin a type (commonly "Tab Widget").
 
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* Fill in the other fields and save.
 
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* Click the create new version and use the naming convention described.  Without this step the plugin will not show up in the plugin list below.
 
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* Make the plugin compatible with "Protege-OWL 4.0".
 
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* When you are done save the page and make sure that your plugin shows up on the [[Protege-OWL_4.0 |4.x version of the Protege-OWL editor]] page.  It seems for some reason this page often does not update for a while so you may need to come back later.
 
  
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==== Handling Problems with FaCT++ not Finding Libraries ====
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* [https://github.com/co-ode-owl-plugins CO-ODE Protege Plugins] - the CO-ODE group at the University of Manchester is the biggest contributor of plug-ins to the Protege editor. The CO-ODE plugins that are compatible with your installation of Protege will show up when going in the File menu -> Check for plugins
  
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On some occasions FaCT++ will have problems
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=== Advertising plug-ins ===
  
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First checkout FaCT++ with the command line call:
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If you have developed a plug-in for Protege and you would like to contribute it to the community,
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svn checkout http://factplusplus.googlecode.com/svn/trunk/ factplusplus.
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please see [[Protege4Contributing#Plugins|contributing plugins]].
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We now need to edit the Makefile.include to use the options associated with the correct version of gcc.  First we find the version of gcc with the command line
 
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gcc -v
 
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On my linux machine the result was
 
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Reading specs from /usr/lib/gcc/i386-redhat-linux/3.4.6/specs
 
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Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-java-awt=gtk --host=i386-redhat-linux
 
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Thread model: posix
 
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gcc version 3.4.6 20060404 (Red Hat 3.4.6-9)
 
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So I modified the Makefile.include so that the GENERAL_DEFINES were
 
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GENERAL_DEFINES = $(GCC_OPT_OPT) $(GCC_34_OPT) $(ALL_DEF)
 
  
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== Wish list ==
 
  
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To follow is list of considerations for improving Protege 4, its documentation, and/or this Wiki.
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== Contributing ==
  
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* Convert [http://www.co-ode.org/resources/tutorials/protege-owl-tutorial.php A Practical Guide Guide to Building Ontologies...] to a collection of Wiki pages so that the guide can be more easily shared, searched, modified, commented on, referenced by section, extended, etc.
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Please see this page for details on how you can [[Protege4Contributing|contribute]].
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* Consider an "Add Tab" feature in the Tabs menu that would allow users to add an empty tab (e.g., "My Tab"), and thus have a place to assemble personal layouts from a clean starting point.  Perhaps provide a minimum of one empty "My Tab" in the user interface.
 

Latest revision as of 14:19, December 22, 2021

Protege Desktop User Documentation

This page is the official documentation home for the Protege Desktop application versions 4, 5 and higher.



Build status & release notes

The latest version of Protege Desktop is 5.5:

You may also download previous versions of Protege and read the complete list of release notes. Older Protege 5.0 beta release notes are available here.

Bugs & feature requests

Before you report a bug or feature request, check the Protege mailing lists archives to ensure it hasn't already been reported. If the item is not currently open or you have further information or a question about an existing item, please post a message on the protege-user mailing list. Give as much detail as possible (including examples or ontologies if possible) as this will help us track things down more quickly.

Current GitHub issue tracker: https://github.com/protegeproject/protege/issues?state=open


Frequently asked questions

We've put together a wiki page to answer the most commonly asked questions about Protege Desktop.


Getting started / tutorials

The Getting started and tutorials have been moved to the main page of the wiki.


Editor features

Advanced features


Further setup / configuration


Plugins

Finding plug-ins

  • Protege will find plugins and updates for you. See our Auto Update page.
  • CO-ODE Protege Plugins - the CO-ODE group at the University of Manchester is the biggest contributor of plug-ins to the Protege editor. The CO-ODE plugins that are compatible with your installation of Protege will show up when going in the File menu -> Check for plugins

Advertising plug-ins

If you have developed a plug-in for Protege and you would like to contribute it to the community, please see contributing plugins.


Contributing

Please see this page for details on how you can contribute.

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