Protege Desktop 5.0 Beta 

[[Image:P5EnhancedSearch.png|thumb|400px|right|Enhanced search capabilities at work in Protege Desktop 5.0 Beta]]

We are very pleased to announce Protege Desktop 5.0 beta!

'''For Users:'''

* [[Install_Protege5|Download and installation instructions]].
* Submit feedback, questions, and/or bug reports on the '''Protege User Support''' mailing list. [http://protege.stanford.edu/support.php#mailingListSupport Sign up for the list] at the Protege website.
* [[ProtegeDesktopUserDocs|Read Protege Desktop documentation]].
* Join the Protege community on [http://www.facebook.com/pages/Protege-Project/136205016405270 Facebook] and [http://www.twitter.com/protegeproject Twitter].

'''For Developers:'''

* Access the source code, file issues, and submit pull requests on GitHub: http://github.com/protegeproject/protege.
* Learn how to [http://github.com/protegeproject/protege/wiki/Building-from-Source build a distribution from source].
* [http://github.com/protegeproject/protege-plugin-examples View example code] for developing tab, view, and menu plug-ins.
* Contact us with your questions on the '''Protege Developer Support''' mailing list. [http://protege.stanford.edu/support.php#mailingListSupport Sign up for the list] at the Protege website.

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== Release Notes ==

''The contents of the release notes section describe changes relative to Protege 4.3.''

=== Build 5.0.0-beta-10 (2014-May-28) ===

==== Enhancements ====
* Moved the [http://github.com/protegeproject/protege Protege Desktop source code] to GitHub to allow for easier collaboration with developers outside of Stanford.
* Moved the Protege Desktop build system to Maven to standardize the build process.
* Upgraded to Java 7.
* Upgraded to the latest version of the OWL API (v3.5.0).
* The search functionality has been significantly improved to search annotation values, display names, entity IRIs, and logical axioms (previously only display name was searched).
* The Individuals tab now filters the list of individuals displayed based on the selected class in the class hierarchy ([http://github.com/protegeproject/protege/issues/1 #1]).
* The UI no longer allows specification of owl:real as the type for a literal ([http://github.com/protegeproject/protege/issues/37 #37]).
* Entering a number into the OWLConstantEditor now parses the value and chooses the correct datatype if no datatype was specified ([http://github.com/protegeproject/protege/issues/42 #42]).
* Exporting DisjointClasses axioms is no longer enabled by default, as this can be an expensive operation ([http://github.com/protegeproject/protege/issues/43 #43]).
* Auto-update only checks for updates once per day, rather than checking for updates every time Protege launches ([http://github.com/protegeproject/protege/issues/45 #45]).
* The Active Ontology tab now shows ontology metrics by default ([http://github.com/protegeproject/protege/issues/46 #46]).

==== Bug Fixes ====
* The inferred object property hierarchy no longer displays owl:bottomObjectProperty as a leaf of every node ([http://github.com/protegeproject/protege/issues/9 #9]).
* Selecting classes in the class hierarchy will only request directly inferred individuals from the reasoner. Previously, Protege requested both direct and indirect inferred individuals, which caused performance issues with larger ontologies ([http://github.com/protegeproject/protege/issues/15 #15]).
* Fixed a bug in the auto-update functionality that caused exceptions when encountering plug-ins with invalid version numbers ([http://github.com/protegeproject/protege/issues/18 #18]).
* Fixed a typo in the DL metrics view ([http://github.com/protegeproject/protege/pull/20 #20]).
* Modified the UI of the Automatic Update dialog to prevent display of an unnecessary trailing '.' character on plug-in version numbers ([http://github.com/protegeproject/protege/issues/23 #23]).
* Fixed an issue that occasionally caused a NullPointerException when opening ontologies ([http://github.com/protegeproject/protege/issues/34 #34]).
* Fixed an issue that occasionally caused the Continue button to remain disabled on the Export Inferred Axioms dialog ([http://github.com/protegeproject/protege/issues/36 #36]).

File:P5EnhancedSearch.png

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Protege 5.0 Beta Release Notes

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ProtegeDesktopUserDocs

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== Protege Desktop User Documentation ==

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

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=== Build status & release notes ===

The latest Protege Desktop build is the '''[[P4_3_Release_Announcement|4.3 release]]''' from April 15, 2013.

To help you decide whether to update, please refer to our [[Protege_Desktop_Old_Versions|complete list of release notes]] for prior versions of Protege.

=== Bugs & feature requests ===

Before you report a bug or feature request, check the lists below 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.

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

Old GForge bug and feature request trackers (no longer in active use):

* [https://bmir-gforge.stanford.edu/gf/project/owleditor/tracker/?action=TrackerItemBrowse&tracker_id=121 Feature request tracker] - a searchable list of features that have been requested (and implemented)
* [https://bmir-gforge.stanford.edu/gf/project/owleditor/tracker/?action=TrackerItemBrowse&tracker_id=118 Bugtracker] - a searchable list of reported and resolved bugs

=== Frequently asked questions ===

We've put together a wiki page to answer the [[Protege-OWL_4_FAQ | most commonly asked questions]] about Protege Desktop.

=== Getting started / tutorials ===

* [[Protege4GettingStarted | Getting started with the Protege-OWL editor]] - a short guide to the interface
* [[Pr4_UG | Protege 4 User's Guide]] - a guide on how to use Protege to create, edit, and inspect ontologies
* [[Protege4Pizzas10Minutes | Pizzas in 10 minutes: A demo of modeling shortcuts]] - a quickstart guide to creating your first OWL ontology
* [http://owl.cs.manchester.ac.uk/tutorials/protegeowltutorial/ A Practical Guide to Building OWL Ontologies using Protege 4 and CO-ODE Tools] - a substantial guide to OWL and ontology engineering
* Cody Burleson's [http://www.semanticfocus.com/blog/entry/title/introduction-to-semantic-web-vision-and-technologies-part-5-building-owl-ontologies-using-protege-4-screencast/ screencast] version of the tutorial listed directly above (it would be great if he got some encouragement for part 6).
* [http://arxiv.org/abs/1201.4089 A Description Logic Primer]

=== Editor features ===

* [[Protege4Features | Overview of features]] - a quick summary of the editor
* [[Protege4Views | P4 views guide]] - a list of all of the default views that are distributed with P4
* [[Protege4Shortcuts | P4 menu guide]] - all of the default menus explained in detail (with keyboard shortcuts)
* [[Protege4Preferences | P4 preferences guide]] - customising P4 to your needs
* [[Protege4NamingAndRendering|Naming and rendering of entities]] - a note on naming things in OWL and configuring P4 to support your naming conventions
* [[Protege4ExpressionEditor | P4 expression editor]] - adding and editing OWL expressions in P4
* [[Manchester_OWL_Syntax|Manchester OWL Syntax]] - an overview of the default syntax used by P4
* [[DLQueryTab | DL Query tab]] - how to query using arbitrary class expressions in OWL
* [[P4AnonymousClasses|Anonymous classes]] - support in P4 for class expressions
* [[Importing_Ontologies_in_P41|OWL Imports]] - modular ontology support in OWL and P4.1
* [[Protege4AxiomAnnotations|Axiom annotations]] - how to annotate at axiom level in Protege 4
* [[Protege4OWLDiff|Protege 4 OWL Diff]] - compare two versions of an ontology

=== Advanced features ===

* [[BeanShell | The Bean Shell]] - Making complex queries against an ontology.
* [[Protege4ClientServer | The Protege 4 Server]]

=== Further setup / configuration ===

* [[ChangingTheHeapSize|Adding more memory]]
* [[EnablingDoubleClick|Double-clicking on OWL files]]
* [[ClearingP4Preferences|Dealing with P4 preferences problems]]
* [[Working with firewalls and proxies]]

=== Plugins ===

==== Finding plug-ins ====

* From build 104 P4 will find plugins and updates for you. See our [[EnablePluginAutoUpdate|Auto Update]] page.

* [[Protege-OWL_4.0 | Plugins for Protege 4.x 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.

* [http://www.co-ode.org/downloads/protege-x/plugins/ CO-ODE Protege 4.x Plugins] - the CO-ODE group at the University of Manchester is the biggest contributor of plug-ins to the Protege-OWL editor. This is a good place to go to download early releases and source code for CO-ODE developed plug-ins.

==== Advertising plug-ins ====

If you have developed a plug-in for Protege-OWL 4.x and you would like to contribute it to the community,
please see [[Protege4Contributing#Plugins|contributing plugins]].

=== Contributing ===

Please see this page for details on how you can [[Protege4Contributing|contribute]].

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#REDIRECT [[ProtegeDesktopUserDocs]]

Protege 5.0 Beta Release Notes

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Install Protege5

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Protege 5.0 Beta Installation Instructions 

Please refer to the specific installation instructions for your platform.

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== Windows ==
Protege 5.0 is distributed in the form of a ZIP file and requires Java 7.

=== Check for Java 7 ===

=== Download the ZIP file ===

* Go to the Products page on the Protege website.
* Click the Download for Windows button.

=== Unzip Protege ===
Once the download completes, navigate to the folder where

=== Launch Protege ===
To launch Protege, double-click the run.bat file in the root directory of the installation.

== Mac OS X ==
Protege 5.0 is distributed in the form of a ZIP file and requires Java 7.

== Unix-like ==
Protege 5.0 is distributed in the form of a tar.gz file and requires Java 7.

File:DLQueryIndividualsOfAClass.gif

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Example of a simple DL Query for individuals of a given class.

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Example of a simple DL Query and result.

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A screenshot of the DL Query tab (shown in MAC OSX Look and Feel)

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DLQueryTab

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Back to [[Protege4UserDocs]]

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= DL Query tab =

[[Image:Protege4DLQueryTab.gif|left|thumb]]
The DL Query tab provides a powerful and easy-to-use feature for searching a classified ontology. It comes with the standard distribution of Protégé Desktop (versions 4.x and above), both as a tab and also as a view widget that can be positioned into any other tab. The query language (''class expression'') supported by the plugin is based on the Manchester OWL syntax, a user-friendly syntax for OWL DL that is fundamentally based on collecting all information about a particular class, property, or individual into a single construct, called a frame.

 

== Getting started ==

[[Image:UnclassifiedVsClassifiedOntology.gif|right]]

If the DL Query tab is unavailable in your Protégé workspace, make sure the DL Query item in the '''Window | Tabs''' menu is checked. Alternatively, you can add the Query view widget to any other tab by selecting '''Window | Views | Query views''' and then placing the widget anywhere in a layout.

You can only execute a query on a classified ontology. Before attempting to execute a query, run a classifier:

* Ensure that one of the built-in reasoners (a.k.a classifiers) is selected. From the Reasoner menu, select FaCT++ or HermiT, then select '''Reasoner | Start Reasoner''' to classify the active ontology. You can also select '''Reasoner | Synchronize reasoner''' (or type Ctrl+R on Windows or Cmd+R on the Mac) to classify again at any time.
* Validate that your ontology is classified by selecting the Entities tab and then the "Class hierarchy (inferred)" tab that appears in the "Class hierarchy" view. It should contain classes that sub-class Thing. If you see only the root class, Thing, your ontology may not be classified. Following is an example comparing what an Inferred Class Hierarchy looks like before and after classification.

* Once you've validated that your ontology is classified, you can execute a query.

 

== Individual query examples ==

[[Image:DLQueryResults.gif|right]]
[[Image:DLQueryIndividualsOfAClass.gif|right]]

Suppose we have an ontology like this:

* Class:
** Person
* Data Properties:
** hasGivenName
** hasSurname

And suppose also that we have several hundred instances of class Person in our ontology. To find an individual named "Matthew", we could enter the following query:

'''hasGivenName value "Matthew"'''

But clicking on the execute button may not return any results. We also need to check the "Individuals" option. Any individuals found will then be displayed in the query results as shown below:

The following query would also be valid for the same result:

'''Person and hasGivenName value "Matthew"'''

We could also show all instances of person by simply providing the class in the query like this:

Of course, these are extremely simple queries; the Manchester syntax is much more capable.

Literal constants can be expressed with type by using ^^ and then the type:

'''hasAge value "21"^^long'''

Or, a more general expression that uses type:

'''hasAge some int'''

Following are just a few more examples to get you going:

'''hasChild some Man'''

'''hasSibling only Woman'''

'''hasCountryOfOrigin value England'''

'''hasChild min 3'''

'''hasChild exactly 3'''

'''hasChild max 3'''

 

== Class query examples ==

Here are some examples of class queries that can be performed on the [http://130.88.198.11/co-ode-files/ontologies/photography.owl ontology of photography] (work in progress).

Firstly, it can be useful to see which things classify "under" this expression.

'''Q: "Which equipment can reduce blur?"'''

We need to get the subclasses of the expression (or descendants if the hierarchy of equipment is deeper than 1 level):
Equipment and reduces some Blur

[[Image:Dl-query-equip-blur2.png]]

Then, we might be interested to see under which existing classes in our hierarchy a given class will classify:

'''Q: "What types of lens is a 35-120mm?"'''

We need to get the superclasses of the expression:
Lens and (hasMinEffectiveFocalLength value 35) and (hasMaxEffectiveFocalLength value 120)

[[Image:Dl-query-lens2.png]]

Other examples might be:

'''Q: "Which adjustments can I use to increase the exposure without affecting the depth of field"'''

We need to get the subclasses of the expression:
Adjustment and increases some ExposureLevel and not(affects some DepthOfField)

[[Image:Dl_query_increase_exposure.png]]

 

== Saving a query in the ontology ==

The DL Query tab becomes a useful way of testing a definition before creating appropriate classes.

If you find a particular query useful and would like to create a class to represent it, you can select the '''Add to ontology''' button.

Protege will display a "Create a new OWLClass" dialog where you enter a class name. Clicking the OK button will then create a defined class in your ontology.

 

== Manchester OWL syntax ==

We have only provided a few simple examples here designed to help you understand how to use the DL Query tab and view widgets. To learn more about the Manchester Syntax, check out these resources:

* [http://www.co-ode.org/resources/reference/manchester_syntax/ The Manchester Syntax] - describes the syntax for class expressions and is aimed at people who already know the previous Protege-OWL compact class expression syntax.
* [[media:Owled2008dc_paper_11.pdf‎|Manchester Syntax for OWL 1.1]] - a more detailed whitepaper (PDF) including revisions for OWL 1.1.
* [http://www.w3.org/2007/OWL/wiki/ManchesterSyntax Manchester Syntax for OWL 2] - the official OWL 2 working group note