Difference between revisions of "Protege-OWL 4 FAQ"

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<span style="font-weight:bold; font-size:20px;">Protege-OWL 4.x Frequently Asked Questions</span>
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__TOC__<br />
  
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== Protege Desktop Frequently Asked Questions ==
  
This page is the FAQ for the '''4.x version of the Protege-OWL editor'''.  We provide the following alternative FAQ pages for other Protege versions and Protege-related topics:
+
<span style="color:red; font-weight:bold;">This FAQ is specific to Protege Desktop, versions 4, 5 and above.</span>
  
* [http://protege.stanford.edu/doc/owl-faq.html Protege-OWL 3.x FAQ]
+
If you're working with older versions of Protege, you might find the following alternative FAQs helpful:
 +
 
 +
* [[Protege-OWL_3_FAQ|Protege-OWL 3.x FAQ]]
 
* [http://protege.stanford.edu/doc/faq.html Protege-Frames FAQ]
 
* [http://protege.stanford.edu/doc/faq.html Protege-Frames FAQ]
 +
* [http://protege.stanford.edu/doc/file_encodings.html Protege file encoding FAQ]
 +
  
 +
=== How do I install Protege Desktop? ===
 +
Protege Desktop is [http://protege.stanford.edu/products.php#desktop-protege available for download] from the main Protege website.  If you're new to Protege, we ask that you read about the different installation options currently available to determine which best suits your needs:
  
__TOC__
+
* '''InstallyAnywhere platform independent installer program''' - this is the recommended method of installation for beginners and also for users that want a "double-clickable" executable file.  The primary reason we recommend this method for beginners is that Protege Desktop requires a 1.6 version of the Java Virtual Machine to be present.  The installer makes it very easy for you to install the correct version of the Java VM - or - if you already have Java installed, you can indicate the location during the install process.  The installer also provides an executable file that you can double-click to launch Protege Desktop, e.g., "Protege.exe" on Windows, etc.
  
 +
* '''ZIP file''' - we provide a ZIP file for more advanced users that are familiar with how to make sure the proper version of Java is present.  This is also a convenient installation for users that do not require an executable file to launch Protege Desktop.
  
=== How do I install Protege-OWL? ===
+
* '''Application bundle file''' - this is a new offering in Protege 4.1 and above that we hope will be an improvement for OS X users.
Protege-OWL is [http://protege.stanford.edu/download/download.html available for download] from the main Protege website. If you are new to Protege-OWL, we ask that you read about the two different installation options currently available to determine which best suits your needs:
 
  
* '''InstallyAnywhere platform independent installer program''' - this is the recommended method of installation for beginners and also for users that want a "double-clickable" executable file.  The primary reason we recommend this method for beginners is that Protege-OWL requires a 1.5 version of the Java Virtual Machine to be present.  The installer makes it very easy for you to install the correct version of the Java VM - or - if you already have Java installed, you can indicate the location during the install process.  The installer also provides an executable file that you can double-click to launch Protege-OWL, e.g., "Protege.exe" on Windows, etc.
+
=== Where can I find user documentation for Protege Desktop? ===
 +
Please refer to the [[Protege4UserDocs#Protege-OWL_Editor|Protege documentation page]] on this wiki for a list of available documentation.
  
* '''ZIP file''' - we provide a ZIP file for more advanced users that are familiar with how to make sure the proper version of Java is presentThis is also a convenient installation for users that do not require an executable file to launch Protege-OWL.
+
=== Where do I ask questions and report bugs? ===
 +
Please post comments, questions, and bug reports on the [http://mailman.stanford.edu/mailman/listinfo/protege-user protege-user mailing list].  Note that you must be subscribed to the list in order to post messagesIf you have difficulties subscribing or unsubscribing from protege-user, please contact the [mailto:protege-user-owner@lists.stanford.edu list owners].
  
* '''Application bundle file''' - we provide an application bundle for OS X users.
+
=== Where can I look at a list known bugs and feature requests? ===
  
Note that if you are new user, we ask that you register before downloading Protege-OWL.  If you have already registered, simply click on the [http://protege.stanford.edu/download/registered.html download link] and navigate to the [http://protege.stanford.edu/download/registered.html#p4 Protege 4 section] of the download page.
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Visit our issue tracker on GitHub: https://github.com/protegeproject/protege/issues?state=open.
  
=== Where can I find user documentation for the Protege-OWL editor? ===
+
=== Why do I get a message about a damaged installer file on the Mac? ===
Please refer to the [[Protege4UserDocs#Protege-OWL_Editor|Protege 4 documentation page]] on this wiki for a list of available documentation.
+
OS X users might see the following error message when trying to install Protege Desktop:
 +
 
 +
 
 +
[[Image:Mac_damaged_installer_error_msg.png]]
  
=== Where do I ask questions and report bugs? ===
 
Please post comments, questions, and bug reports about Protege-OWL on the [http://mailman.stanford.edu/mailman/listinfo/p4-feedback p4-feedback mailing list].  Note that you must be subscribed to this list in order to post messages.  Instructions for subscribing to Protege mailing lists are [http://protege.stanford.edu/doc/faq.html#01a.02 available on the main Protege website].  If you have difficulties subscribing or unsubscribing from p4-feedback, please contact the [mailto:p4-feedback-owner@lists.stanford.edu list owners].
 
  
=== Where can I look at a list known bugs and feature requests? ===
+
This is a misleading error message from Apple's [http://support.apple.com/kb/ht5290 Gatekeeper] software.  By default, Gatekeeper is configured to only allow download and installation of applications from the Mac App Store and identified developers. The Protege Desktop software does not yet carry "identified developer" status. To successfully install Protege Desktop, navigate to Apple menu | System Preferences… | Security & Privacy | General tab, and select "Anywhere" from "Allow applications downloaded from".
* View [https://bmir-gforge.stanford.edu/gf/project/owleditor/tracker/?action=TrackerItemBrowse&tracker_id=118 bug database]
 
* View [https://bmir-gforge.stanford.edu/gf/project/owleditor/tracker/?action=TrackerItemBrowse&tracker_id=121 feature request list]
 
  
 
=== Why am I getting "An error related to DOT has occurred" when trying to use the OWLViz plug-in? ===
 
=== Why am I getting "An error related to DOT has occurred" when trying to use the OWLViz plug-in? ===
 
If you see this error when trying to use OWLViz, it means that you have not completed some of the necessary steps to configure this plug-in.  Complete documentation for fixing this error is available in the [http://protegewiki.stanford.edu/index.php/OWLViz#Troubleshooting troubleshooting section] of the OWLViz documentation.
 
If you see this error when trying to use OWLViz, it means that you have not completed some of the necessary steps to configure this plug-in.  Complete documentation for fixing this error is available in the [http://protegewiki.stanford.edu/index.php/OWLViz#Troubleshooting troubleshooting section] of the OWLViz documentation.
 +
 +
=== How do I change the name of an entity (class, property, individual) in my ontology? ===
 +
Select the Refactor | Change entity URI... menu item.  In the resulting Change entity URI dialog box, enter the new name in the text box, and click the OK button.
 +
 +
=== Why does my ontology contain classes named Error1, Error2, ...? ===
 +
See the [[Protege4ErrorClasses|Error Classes]] page for a description of this new OWL API feature.
 +
 +
=== How do I edit/use SWRL rules in Protege ===
 +
* Create a new tab (Window -> Views -> Create new tab...) called something like Rules, SWRL or whatever you prefer [OPTIONAL]
 +
* Select the Window -> Views -> Ontology views -> Rules menu and drop the "Rules" view in a tab (for example the one created in the previous step)
 +
* Different reasoners have different level of support for rules. Pellet has the best support for SWRL rules. If you don't see Pellet listed in your Reasoner menu, install it (Open Files -> Preferences, select Plugins tab, press on "Check for downloads now" button, select and install Pellet) 
 +
* In the Reasoner menu select the the Pellet reasoner [IMPORTANT]
 +
* View/Create/Edit/Delete SWRL rules in the "Rules" view
 +
* Start (Reasoner -> Start reasoner) or synchronize (Reasoner -> Synchronize reasoner) the reasoner (you can also do it with CTRL+R or COMMAND+R on Mac)
 +
* See results of the execurted rules in you other views
 +
 +
=== What are the pros and cons of DL Query, SPARQL (with OWL entailment regime), and SQWRL===
 +
A DL Query is a OWL class expression. It
 +
* Returns results that can be superclasses, subclasses, or individuals of the class expression.
 +
* Has compact notation
 +
* Cannot use variables, therefore cannot compare values from different properties e.g., (forall all individuals ?x of class C where ?x.length = ?x.width)
 +
* Has limited sets of operators (e.g., can use regular expressions on strings but cannot do arithmetic)
 +
* Uses open-world assumption
 +
* Resolves queries relative to import closure, does not support federated queries
 +
* Is supported by any OWL reasoning system (Protege has GUI for DL queries)
 +
 +
SPARQL query is a graph pattern. It
 +
* Can match against anything against graph patterns.
 +
* Has a rich set of operators and functions on numbers, strings, date/time, and terms
 +
* Is widely supported (although not all SPARQL engine support OWL2 entailment regime)
 +
* Can be resolved against relational databases with mappings (e.g., Ontop)
 +
* Supports federated queries across the net
 +
* Can work with OWL ontology because of formalized OWL to RDF mapping. Complex class expressions have very verbose RDF representation.
 +
 +
SQWRL is an extension of OWL/SWRL. It
 +
* Natively understands OWL
 +
* Allows you to query for individuals only
 +
* Has an extensible collection of built-ins (including the ability to do arithmetic)
 +
* Has set operators that “close the world”
 +
* Allows comparison of values of different properties on the same individual
 +
* Is supported by Protege only
 +
* Does not support federated queries across the net

Revision as of 14:18, August 17, 2016


Protege Desktop Frequently Asked Questions

This FAQ is specific to Protege Desktop, versions 4, 5 and above.

If you're working with older versions of Protege, you might find the following alternative FAQs helpful:


How do I install Protege Desktop?

Protege Desktop is available for download from the main Protege website. If you're new to Protege, we ask that you read about the different installation options currently available to determine which best suits your needs:

  • InstallyAnywhere platform independent installer program - this is the recommended method of installation for beginners and also for users that want a "double-clickable" executable file. The primary reason we recommend this method for beginners is that Protege Desktop requires a 1.6 version of the Java Virtual Machine to be present. The installer makes it very easy for you to install the correct version of the Java VM - or - if you already have Java installed, you can indicate the location during the install process. The installer also provides an executable file that you can double-click to launch Protege Desktop, e.g., "Protege.exe" on Windows, etc.
  • ZIP file - we provide a ZIP file for more advanced users that are familiar with how to make sure the proper version of Java is present. This is also a convenient installation for users that do not require an executable file to launch Protege Desktop.
  • Application bundle file - this is a new offering in Protege 4.1 and above that we hope will be an improvement for OS X users.

Where can I find user documentation for Protege Desktop?

Please refer to the Protege documentation page on this wiki for a list of available documentation.

Where do I ask questions and report bugs?

Please post comments, questions, and bug reports on the protege-user mailing list. Note that you must be subscribed to the list in order to post messages. If you have difficulties subscribing or unsubscribing from protege-user, please contact the list owners.

Where can I look at a list known bugs and feature requests?

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

Why do I get a message about a damaged installer file on the Mac?

OS X users might see the following error message when trying to install Protege Desktop:


Mac damaged installer error msg.png


This is a misleading error message from Apple's Gatekeeper software. By default, Gatekeeper is configured to only allow download and installation of applications from the Mac App Store and identified developers. The Protege Desktop software does not yet carry "identified developer" status. To successfully install Protege Desktop, navigate to Apple menu | System Preferences… | Security & Privacy | General tab, and select "Anywhere" from "Allow applications downloaded from".

Why am I getting "An error related to DOT has occurred" when trying to use the OWLViz plug-in?

If you see this error when trying to use OWLViz, it means that you have not completed some of the necessary steps to configure this plug-in. Complete documentation for fixing this error is available in the troubleshooting section of the OWLViz documentation.

How do I change the name of an entity (class, property, individual) in my ontology?

Select the Refactor | Change entity URI... menu item. In the resulting Change entity URI dialog box, enter the new name in the text box, and click the OK button.

Why does my ontology contain classes named Error1, Error2, ...?

See the Error Classes page for a description of this new OWL API feature.

How do I edit/use SWRL rules in Protege

  • Create a new tab (Window -> Views -> Create new tab...) called something like Rules, SWRL or whatever you prefer [OPTIONAL]
  • Select the Window -> Views -> Ontology views -> Rules menu and drop the "Rules" view in a tab (for example the one created in the previous step)
  • Different reasoners have different level of support for rules. Pellet has the best support for SWRL rules. If you don't see Pellet listed in your Reasoner menu, install it (Open Files -> Preferences, select Plugins tab, press on "Check for downloads now" button, select and install Pellet)
  • In the Reasoner menu select the the Pellet reasoner [IMPORTANT]
  • View/Create/Edit/Delete SWRL rules in the "Rules" view
  • Start (Reasoner -> Start reasoner) or synchronize (Reasoner -> Synchronize reasoner) the reasoner (you can also do it with CTRL+R or COMMAND+R on Mac)
  • See results of the execurted rules in you other views

What are the pros and cons of DL Query, SPARQL (with OWL entailment regime), and SQWRL

A DL Query is a OWL class expression. It

  • Returns results that can be superclasses, subclasses, or individuals of the class expression.
  • Has compact notation
  • Cannot use variables, therefore cannot compare values from different properties e.g., (forall all individuals ?x of class C where ?x.length = ?x.width)
  • Has limited sets of operators (e.g., can use regular expressions on strings but cannot do arithmetic)
  • Uses open-world assumption
  • Resolves queries relative to import closure, does not support federated queries
  • Is supported by any OWL reasoning system (Protege has GUI for DL queries)

SPARQL query is a graph pattern. It

  • Can match against anything against graph patterns.
  • Has a rich set of operators and functions on numbers, strings, date/time, and terms
  • Is widely supported (although not all SPARQL engine support OWL2 entailment regime)
  • Can be resolved against relational databases with mappings (e.g., Ontop)
  • Supports federated queries across the net
  • Can work with OWL ontology because of formalized OWL to RDF mapping. Complex class expressions have very verbose RDF representation.

SQWRL is an extension of OWL/SWRL. It

  • Natively understands OWL
  • Allows you to query for individuals only
  • Has an extensible collection of built-ins (including the ability to do arithmetic)
  • Has set operators that “close the world”
  • Allows comparison of values of different properties on the same individual
  • Is supported by Protege only
  • Does not support federated queries across the net