Protege Wiki - User contributions [en]

Main Page

2019-08-06T17:49:38Z

Matthewhorridge: /* WebProtégé */

__NOTOC__
= Welcome to the Protégé wiki! =

[[File:WP-classes.png|right|300px|thumb|[[WebProtege|WebProtégé]] - a powerful collaborative ontology development environment for the Web ]]

[[File:Protege-OWL.jpg|right|300px|thumb|[[Protege4UserDocs|Protégé Desktop]] - a fully-fledged OWL 2 ontology editor for the desktops]]

[http://protege.stanford.edu Protégé] is a free, open-source platform that provides a growing user community with a suite of tools to construct domain models and knowledge-based applications with ontologies.

''' Quick links: [http://webprotege.stanford.edu WebProtégé server], Protégé Desktop [http://protege.stanford.edu/products.php#desktop-protege download] and [https://github.com/protegeproject/protege-distribution/releases release notes], [https://github.com/protegeproject/ Source code on GitHub], [http://protege.stanford.edu Protégé website] '''

= User Documentation =

=== WebProtégé ===
* [[WebProtege|Overview]]
* [[WebProtegeUsersGuide|User's Guide]]
* [https://github.com/protegeproject/webprotege/wiki/WebProtégé-4.0.0-beta-x-Installation Administrator's Guide] - download and installation instructions
* Use WebProtégé now on our Stanford-hosted server: http://webprotege.stanford.edu

=== Protégé Desktop ===
* [[Protege4UserDocs|Protégé Desktop documentation]] ([https://github.com/protegeproject/protege-distribution/releases release notes], [[Install_Protege5|installation instructions]], [http://protege.stanford.edu/products.php#desktop-protege Protege Desktop download], [[Protege_Desktop_Old_Versions|older Protege releases download]])
* [[Protege3UserDocs|Older Protégé releases documentation (version 3.x)]]
* [[Protege-OWL_4_FAQ|Frequently Asked Questions (FAQ)]]

=== Tutorials and Getting Started ===
* [http://protege.stanford.edu/publications/ontology_development/ontology101.html Ontology Development 101: A Guide to creating your first ontology]
* [http://www.cs.man.ac.uk/~stevensr/menupages/background.php Brief introduction to ontologies], by Robert Stevens
* [http://owl.cs.manchester.ac.uk/publications/talks-and-tutorials/protg-owl-tutorial/ Protégé OWL Tutorial: A step-by-step guide to modeling in OWL using the Protégé OWL tools]
* Semantic Web Best Practices and Deployment Working Group's [http://www.w3.org/2001/sw/BestPractices/Tutorials Semantic Web Tutorials] page
* [[Protege4GettingStarted | Getting started with the Protege Desktop editor]] - a short guide to the interface
* [[Pr4_UG | Protege Desktop 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
* 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 Protege OWL Pizza tutorial (listed above).
* [http://arxiv.org/abs/1201.4089 A Description Logic Primer]

= Developer Documentation =

=== WebProtégé ===

Please see the [https://github.com/protegeproject/webprotege WebProtégé GitHub page]

=== Protégé Desktop ===
* [[Protege5DevDocs|Protégé Desktop 5.x]]
* [[Protege4DevDocs|Protégé Desktop 4.x]]
* [[Protege3DevDocs|Protégé Desktop 3.x]]

* [[ProtegeQAGuide|Guide to Quality Assurance]]

= Download and Support =

To download Protégé or WebProtégé please visit our [http://protege.stanford.edu homepage]. To use the WebProtégé server hosted at Stanford, please go to: http://webprotege.stanford.edu.

To find out about the different support options, for example, how to subscribe to our mailing lists, please visit the [http://protege.stanford.edu/support.php Support page].

Follow our [http://www.youtube.com/user/TheProtegeProject YouTube channel] featuring screencasts showing different features of Protégé and WebProtégé.

= Wiki Help =
If you are new to using a Wiki, please see the [[Help:Contents|Help page]] page for links to User's Guides, etc.

The [[Help:Contents|Help page]] also has suggestions for where to find help with using the Protégé application.

WebProtege

2019-08-06T17:48:41Z

Matthewhorridge: /* Administrator's Guide */

WebProtégé 

[[File:WP-classes.png|thumb|400px|right|text-bottom|The new WebProtégé with simplified editing and improved collaboration support]]

'''WebProtégé is a free, open source collaborative ontology development environment for the Web. '''

We encourage end users to use our hosted solution at: '''http://webprotege.stanford.edu'''. Alternatively, WebProtégé can be [[WebProtegeAdminGuide|downloaded and installed]] on your own server.

'''WebProtégé provides the following features:'''
* Support for editing OWL 2 ontologies
* A default simple editing interface, which provides access to commonly used OWL constructs
* Full change tracking and revision history
* Collaboration tools such as, sharing and permissions, threaded notes and discussions, watches and email notifications
* Customizable user interface
* Customizable Web forms for application/domain specific editing
* Support for editing OBO ontologies
* Multiple formats for upload and download of ontologies (supported formats: RDF/XML, Turtle, OWL/XML, OBO, and others)

 [https://github.com/protegeproject/webprotege '''Source code on GitHub''']  
 [https://github.com/protegeproject/webprotege/releases '''Latest release and release notes'''] 

<div style="background: #FDECE7; border: 2px solid #AE5B08; padding: 10px 15px 10px 20px; margin: 30px 430px 0 0; ">

'''Use [http://webprotege.stanford.edu WebProtégé] now on our Stanford-hosted server!''' http://webprotege.stanford.edu

</div>

 
__NOTOC__
== Documentation ==

=== [[WebProtegeUsersGuide|User's Guide]] ===
A short [[WebProtegeUsersGuide|user guide]] with screencasts and screenshots describing the main user interface elements in WebProtégé.

=== Administrator's Guide ===
A [https://github.com/protegeproject/webprotege/wiki/WebProtégé-4.0.0-beta-x-Installation step-by-step guide] for site administrators who want to download and install WebProtégé.

== About WebProtégé ==
WebProtégé is being actively developed by the [http://protege.stanford.edu/about.php Protégé team] at the [[Affiliated with::Stanford Center for Biomedical Informatics Research]]. WebProtégé is free and open source under [https://github.com/protegeproject/webprotege/blob/master/license.txt BSD 2-clause] license.

== References ==

* A WebProtégé paper describing its architecture, features and use in real-world cases is published in the Semantic Web Journal, and is available [http://www.semantic-web-journal.net/content/webprot%C3%A9g%C3%A9-distributed-ontology-editor-and-knowledge-acquisition-tool-web here].

* Several papers describing the use of WebProtégé in real use cases can be found [http://www.informatik.uni-trier.de/~ley/pers/hd/t/Tudorache:Tania here].

== How to cite WebProtégé ==

Tudorache, Tania, Csongor Nyulas, Natalya F. Noy, and Mark A. Musen. "WebProtégé: A collaborative ontology editor and knowledge acquisition tool for the web." Semantic web 4, no. 1 (2013): 89-99.

Online version available [http://www.semantic-web-journal.net/content/webprot%C3%A9g%C3%A9-distributed-ontology-editor-and-knowledge-acquisition-tool-web here].

== Contact Us ==
If you have questions or comments, please post them on the [http://protege.stanford.edu/support.php Protégé mailing lists]. 

[[Category:Application]]
[[Category:WebProtege documentation]]

WebProtege

2019-08-06T17:48:28Z

Matthewhorridge: /* Download and Install - Administrator's Guide */

WebProtégé 

[[File:WP-classes.png|thumb|400px|right|text-bottom|The new WebProtégé with simplified editing and improved collaboration support]]

'''WebProtégé is a free, open source collaborative ontology development environment for the Web. '''

We encourage end users to use our hosted solution at: '''http://webprotege.stanford.edu'''. Alternatively, WebProtégé can be [[WebProtegeAdminGuide|downloaded and installed]] on your own server.

'''WebProtégé provides the following features:'''
* Support for editing OWL 2 ontologies
* A default simple editing interface, which provides access to commonly used OWL constructs
* Full change tracking and revision history
* Collaboration tools such as, sharing and permissions, threaded notes and discussions, watches and email notifications
* Customizable user interface
* Customizable Web forms for application/domain specific editing
* Support for editing OBO ontologies
* Multiple formats for upload and download of ontologies (supported formats: RDF/XML, Turtle, OWL/XML, OBO, and others)

 [https://github.com/protegeproject/webprotege '''Source code on GitHub''']  
 [https://github.com/protegeproject/webprotege/releases '''Latest release and release notes'''] 

<div style="background: #FDECE7; border: 2px solid #AE5B08; padding: 10px 15px 10px 20px; margin: 30px 430px 0 0; ">

'''Use [http://webprotege.stanford.edu WebProtégé] now on our Stanford-hosted server!''' http://webprotege.stanford.edu

</div>

 
__NOTOC__
== Documentation ==

=== [[WebProtegeUsersGuide|User's Guide]] ===
A short [[WebProtegeUsersGuide|user guide]] with screencasts and screenshots describing the main user interface elements in WebProtégé.

=== Administrator's Guide ===
A [[https://github.com/protegeproject/webprotege/wiki/WebProtégé-4.0.0-beta-x-Installation step-by-step guide]] for site administrators who want to download and install WebProtégé.

== About WebProtégé ==
WebProtégé is being actively developed by the [http://protege.stanford.edu/about.php Protégé team] at the [[Affiliated with::Stanford Center for Biomedical Informatics Research]]. WebProtégé is free and open source under [https://github.com/protegeproject/webprotege/blob/master/license.txt BSD 2-clause] license.

== References ==

* A WebProtégé paper describing its architecture, features and use in real-world cases is published in the Semantic Web Journal, and is available [http://www.semantic-web-journal.net/content/webprot%C3%A9g%C3%A9-distributed-ontology-editor-and-knowledge-acquisition-tool-web here].

* Several papers describing the use of WebProtégé in real use cases can be found [http://www.informatik.uni-trier.de/~ley/pers/hd/t/Tudorache:Tania here].

== How to cite WebProtégé ==

Tudorache, Tania, Csongor Nyulas, Natalya F. Noy, and Mark A. Musen. "WebProtégé: A collaborative ontology editor and knowledge acquisition tool for the web." Semantic web 4, no. 1 (2013): 89-99.

Online version available [http://www.semantic-web-journal.net/content/webprot%C3%A9g%C3%A9-distributed-ontology-editor-and-knowledge-acquisition-tool-web here].

== Contact Us ==
If you have questions or comments, please post them on the [http://protege.stanford.edu/support.php Protégé mailing lists]. 

[[Category:Application]]
[[Category:WebProtege documentation]]

WebProtege

2019-08-06T17:47:02Z

Matthewhorridge: /* Documentation */

WebProtégé 

[[File:WP-classes.png|thumb|400px|right|text-bottom|The new WebProtégé with simplified editing and improved collaboration support]]

'''WebProtégé is a free, open source collaborative ontology development environment for the Web. '''

We encourage end users to use our hosted solution at: '''http://webprotege.stanford.edu'''. Alternatively, WebProtégé can be [[WebProtegeAdminGuide|downloaded and installed]] on your own server.

'''WebProtégé provides the following features:'''
* Support for editing OWL 2 ontologies
* A default simple editing interface, which provides access to commonly used OWL constructs
* Full change tracking and revision history
* Collaboration tools such as, sharing and permissions, threaded notes and discussions, watches and email notifications
* Customizable user interface
* Customizable Web forms for application/domain specific editing
* Support for editing OBO ontologies
* Multiple formats for upload and download of ontologies (supported formats: RDF/XML, Turtle, OWL/XML, OBO, and others)

 [https://github.com/protegeproject/webprotege '''Source code on GitHub''']  
 [https://github.com/protegeproject/webprotege/releases '''Latest release and release notes'''] 

<div style="background: #FDECE7; border: 2px solid #AE5B08; padding: 10px 15px 10px 20px; margin: 30px 430px 0 0; ">

'''Use [http://webprotege.stanford.edu WebProtégé] now on our Stanford-hosted server!''' http://webprotege.stanford.edu

</div>

 
__NOTOC__
== Documentation ==

=== [[WebProtegeUsersGuide|User's Guide]] ===
A short [[WebProtegeUsersGuide|user guide]] with screencasts and screenshots describing the main user interface elements in WebProtégé.

=== [[WebProtegeAdminGuide|Download and Install - Administrator's Guide]] ===
A [[WebProtegeAdminGuide|step-by-step guide]] for site administrators who want to download and install WebProtégé.

== About WebProtégé ==
WebProtégé is being actively developed by the [http://protege.stanford.edu/about.php Protégé team] at the [[Affiliated with::Stanford Center for Biomedical Informatics Research]]. WebProtégé is free and open source under [https://github.com/protegeproject/webprotege/blob/master/license.txt BSD 2-clause] license.

== References ==

* A WebProtégé paper describing its architecture, features and use in real-world cases is published in the Semantic Web Journal, and is available [http://www.semantic-web-journal.net/content/webprot%C3%A9g%C3%A9-distributed-ontology-editor-and-knowledge-acquisition-tool-web here].

* Several papers describing the use of WebProtégé in real use cases can be found [http://www.informatik.uni-trier.de/~ley/pers/hd/t/Tudorache:Tania here].

== How to cite WebProtégé ==

Tudorache, Tania, Csongor Nyulas, Natalya F. Noy, and Mark A. Musen. "WebProtégé: A collaborative ontology editor and knowledge acquisition tool for the web." Semantic web 4, no. 1 (2013): 89-99.

Online version available [http://www.semantic-web-journal.net/content/webprot%C3%A9g%C3%A9-distributed-ontology-editor-and-knowledge-acquisition-tool-web here].

== Contact Us ==
If you have questions or comments, please post them on the [http://protege.stanford.edu/support.php Protégé mailing lists]. 

[[Category:Application]]
[[Category:WebProtege documentation]]

Main Page

2019-08-06T17:40:39Z

Matthewhorridge: /* WebProtégé */

__NOTOC__
= Welcome to the Protégé wiki! =

[[File:WP-classes.png|right|300px|thumb|[[WebProtege|WebProtégé]] - a powerful collaborative ontology development environment for the Web ]]

[[File:Protege-OWL.jpg|right|300px|thumb|[[Protege4UserDocs|Protégé Desktop]] - a fully-fledged OWL 2 ontology editor for the desktops]]

[http://protege.stanford.edu Protégé] is a free, open-source platform that provides a growing user community with a suite of tools to construct domain models and knowledge-based applications with ontologies.

''' Quick links: [http://webprotege.stanford.edu WebProtégé server], Protégé Desktop [http://protege.stanford.edu/products.php#desktop-protege download] and [https://github.com/protegeproject/protege-distribution/releases release notes], [https://github.com/protegeproject/ Source code on GitHub], [http://protege.stanford.edu Protégé website] '''

= User Documentation =

=== WebProtégé ===
* [[WebProtege|Overview]]
* [[WebProtegeUsersGuide|User's Guide]]
* [[WebProtegeAdminGuide|Administrator's Guide]] - download and installation instructions
* Use WebProtégé now on our Stanford-hosted server: http://webprotege.stanford.edu

=== Protégé Desktop ===
* [[Protege4UserDocs|Protégé Desktop documentation]] ([https://github.com/protegeproject/protege-distribution/releases release notes], [[Install_Protege5|installation instructions]], [http://protege.stanford.edu/products.php#desktop-protege Protege Desktop download], [[Protege_Desktop_Old_Versions|older Protege releases download]])
* [[Protege3UserDocs|Older Protégé releases documentation (version 3.x)]]
* [[Protege-OWL_4_FAQ|Frequently Asked Questions (FAQ)]]

=== Tutorials and Getting Started ===
* [http://protege.stanford.edu/publications/ontology_development/ontology101.html Ontology Development 101: A Guide to creating your first ontology]
* [http://www.cs.man.ac.uk/~stevensr/menupages/background.php Brief introduction to ontologies], by Robert Stevens
* [http://owl.cs.manchester.ac.uk/publications/talks-and-tutorials/protg-owl-tutorial/ Protégé OWL Tutorial: A step-by-step guide to modeling in OWL using the Protégé OWL tools]
* Semantic Web Best Practices and Deployment Working Group's [http://www.w3.org/2001/sw/BestPractices/Tutorials Semantic Web Tutorials] page
* [[Protege4GettingStarted | Getting started with the Protege Desktop editor]] - a short guide to the interface
* [[Pr4_UG | Protege Desktop 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
* 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 Protege OWL Pizza tutorial (listed above).
* [http://arxiv.org/abs/1201.4089 A Description Logic Primer]

= Developer Documentation =

=== WebProtégé ===

Please see the [https://github.com/protegeproject/webprotege WebProtégé GitHub page]

=== Protégé Desktop ===
* [[Protege5DevDocs|Protégé Desktop 5.x]]
* [[Protege4DevDocs|Protégé Desktop 4.x]]
* [[Protege3DevDocs|Protégé Desktop 3.x]]

* [[ProtegeQAGuide|Guide to Quality Assurance]]

= Download and Support =

To download Protégé or WebProtégé please visit our [http://protege.stanford.edu homepage]. To use the WebProtégé server hosted at Stanford, please go to: http://webprotege.stanford.edu.

To find out about the different support options, for example, how to subscribe to our mailing lists, please visit the [http://protege.stanford.edu/support.php Support page].

Follow our [http://www.youtube.com/user/TheProtegeProject YouTube channel] featuring screencasts showing different features of Protégé and WebProtégé.

= Wiki Help =
If you are new to using a Wiki, please see the [[Help:Contents|Help page]] page for links to User's Guides, etc.

The [[Help:Contents|Help page]] also has suggestions for where to find help with using the Protégé application.

Install Protege5 Mac

2016-05-24T23:03:32Z

Matthewhorridge:

= [[File:Mac-logo.jpg|50px]] Protege 5 Installation instructions for MacOSX =

__TOC__

'''[[Install_Protege5|Go to the main Protege 5 installation page]]'''

Protege Desktop 5.0 is distributed in the form of a ZIP file from the [http://protege.stanford.edu/products.php#desktop-protege main Protege website], and includes the 64-bit Java Runtime Environment (JRE). So, it is not necessary to have Java pre-installed on your computer to run Protege.

== Download the ZIP file ==
* Go to the [http://protege.stanford.edu/products.php#desktop-protege Products page] on the Protege website.
* Click the "Download for Mac OSX" button to download the ZIP file to your machine.

== Move Protege to Applications ==
* Once the download completes, navigate to the folder where the ZIP file was unpacked. On a Mac, this will typically be your "Downloads" folder:

[[File:protege-app-bundle.png]]

Drag the Protege_5.0_beta folder to the Applications directory.

== Launch Protege ==
To launch Protege Desktop, double-click the <code>run.command</code> file in the root directory of the installation (<code>Applications/Protege_5.0_beta/run.command</code>).

== Allow Protege to run ==
The first time you will try to run the <code>run.command</code>, you will get a warning:

[[File:MacOXWarningProtegeApp.png]]

To allow Protege to run, go to your ''System Preferences'' (in the dock, or in Finder->Applications->System Preferences), and go to the ''Security & Privacy'', and then the ''General'' tab. It will look like this:

[[File:MacOSXSecurityPrefs.png]]

Click on the button ''Open anyway'' and you will get to another dialog, like:

[[File:MacOSXWarning2.png]]

Click on ''Open'' and Protege will start.

Alternatively, you may also select for the ''Allow apps downloaded from:'' the checkbox: ''Anywhere'' in the ''Security & Privacy'' preferences panel.

= Troubleshooting =

''Q'': ''When I double-click on the run script, nothing happens, or I see a window that comes up, and goes away!''

''A'': Try running Protege from a console and report any errors displayed in the console window on the [http://protege.stanford.edu/support.php#mailingListSupport Protege User Support mailing list].

* How to run Protege from the console on OS X:
** Open Finder
** Select Applications -> Utilities, then double-click on the Terminal application
** In the resulting Terminal window, change to the directory where you unzipped Protege (e.g., <code>cd /Applications/Protege_5.0_beta</code>)
** Type <code>sh run.command</code>

Then report the results back on the [http://protege.stanford.edu/support.php protege-user] mailing list.

'''[[Install_Protege5|Go to the main Protege 5 installation page]]'''

Install Protege5 Mac

2016-05-24T23:02:14Z

Matthewhorridge:

= [[File:Mac-logo.jpg|50px]] Protege 5 Installation instructions for MacOSX =

__TOC__

'''[[Install_Protege5|Go to the main Protege 5 installation page]]'''

Protege Desktop 5.0 is distributed in the form of a ZIP file from the [http://protege.stanford.edu/products.php#desktop-protege main Protege website], and includes the 64-bit Java Runtime Environment (JRE). So, it is not necessary to have Java pre-installed on your computer to run Protege.

== Download the ZIP file ==
* Go to the [http://protege.stanford.edu/products.php#desktop-protege Products page] on the Protege website.
* Click the "Download for Mac OSX" button to download the ZIP file to your machine.

== Move Protege to Applications ==
* Once the download completes, navigate to the folder where the ZIP file was unpacked. On a Mac, this will typically be your "Downloads" folder:

[[File:protege-app-bundle.jpg]]

Drag the Protege_5.0_beta folder to the Applications directory.

== Launch Protege ==
To launch Protege Desktop, double-click the <code>run.command</code> file in the root directory of the installation (<code>Applications/Protege_5.0_beta/run.command</code>).

== Allow Protege to run ==
The first time you will try to run the <code>run.command</code>, you will get a warning:

[[File:MacOXWarningProtegeApp.png]]

To allow Protege to run, go to your ''System Preferences'' (in the dock, or in Finder->Applications->System Preferences), and go to the ''Security & Privacy'', and then the ''General'' tab. It will look like this:

[[File:MacOSXSecurityPrefs.png]]

Click on the button ''Open anyway'' and you will get to another dialog, like:

[[File:MacOSXWarning2.png]]

Click on ''Open'' and Protege will start.

Alternatively, you may also select for the ''Allow apps downloaded from:'' the checkbox: ''Anywhere'' in the ''Security & Privacy'' preferences panel.

= Troubleshooting =

''Q'': ''When I double-click on the run script, nothing happens, or I see a window that comes up, and goes away!''

''A'': Try running Protege from a console and report any errors displayed in the console window on the [http://protege.stanford.edu/support.php#mailingListSupport Protege User Support mailing list].

* How to run Protege from the console on OS X:
** Open Finder
** Select Applications -> Utilities, then double-click on the Terminal application
** In the resulting Terminal window, change to the directory where you unzipped Protege (e.g., <code>cd /Applications/Protege_5.0_beta</code>)
** Type <code>sh run.command</code>

Then report the results back on the [http://protege.stanford.edu/support.php protege-user] mailing list.

'''[[Install_Protege5|Go to the main Protege 5 installation page]]'''

File:Protege-app-bundle.png

2016-05-24T23:01:34Z

Matthewhorridge:

User talk:Phillord

2014-06-16T16:32:30Z

Matthewhorridge: Welcome!

'''Welcome to ''Protege Wiki''!'''
We hope you will contribute much and well.
You will probably want to read the [[Help:Contents|help pages]].
Again, welcome and have fun! [[User:Matthewhorridge|Matthewhorridge]] ([[User talk:Matthewhorridge|talk]]) 09:32, June 16, 2014 (PDT)

User:Phillord

2014-06-16T16:32:30Z

Matthewhorridge: Creating user page for new user.

Read all about me on these other web pages.

http://homepages.cs.ncl.ac.uk/phillip.lord/
http://ontogenesis.knowledgeblog.org

Also try out Tawny-OWL which provides a totally new ontology development experience.

https://github.com/phillord/tawny-owl

My research covers a variety of different areas; mostly it focuses on the use of ontological technology in biology, or more generally mechanisms for presenting and publishing scientific information. I am currently developing Tawny-OWL, a library which allows fully programmatic development of ontologies. Development and application of this library is covered in my journal.

I also developed the idea of the Knowledge Blog which has been supported by Ontogenesis Network, and has resulted in the start of a Ontology Encyclopedia. Part of this work recently appeared on the Guardian science blogs. You can read many of my papers and current research in my journal.

WebProtegeUsersGuide

2014-03-17T23:08:19Z

Matthewhorridge:

WebProtégé User Guide

'''WebProtégé''' is an open source, lightweight, web-based ontology editor.

__TOC__

'''Looking for the user guide of the old WebProtege (release 1.0)? [[WebProtege1.0UsersGuide|Here it is]].'''

'''Go back to [[WebProtege|WebProtégé main page]].'''

= Screencasts =

[[File:WP-screencast.png|thumb|70px|left|link=http://www.youtube.com/watch?v=QvURiHVXnQQ]]

You can watch a [http://www.youtube.com/watch?v=QvURiHVXnQQ 15 minutes screencast] that introduces the features of the new WebProtege (creating and uploading ontologies, sharing with collaborators, simplified editing with auto-completion, etc.).

You may also watch a [http://videolectures.net/iswc2013_horridge_webprotege/ 15 minutes presentation] of the simplified user interface of WebProtege and how we came to it that was presented at [http://iswc2013.semanticweb.org/ ISWC 2013].

A more comprehensive [https://stanford.webex.com/stanford/lsr.php?AT=pb&SP=MC&rID=62510447&rKey=13018bdbb414ba08 one-hour long screencast] showing also the OBO editing, and the support for linking to BioPortal is available on the [http://www.bioontology.org/ontology-editing-and-publishing-using-webprotege-and-bioportal NCBO Webinar webpage].

= Home Screen =

When you open http://webprotege.stanford.edu in a browser you should see the list of public projects and various links to create an account or sign in (top right). You can download the ontologies in any publicly available project by clicking the download icon in the table. To open a project click on its name in the Project Name column.

[[File:wp-home-screen.png|800px]]

To create and upload your own projects you need to have a user account and be signed in. If you don't have a user account you can create one using the ''Sign Up for Account'' button. To sign in click the ''Sign In'' link in the top right of the browser window. Enter your user name and password in the dialog that pops up. (You can also sign in with OpenId).

== Nav Bar ==

[[File:Wp-nav-bar.png]]

Once you are signed in you will see a side bar on the left hand side of the screen which offers different categories of projects to view. Clicking on any item in the side bar will filter the list of projects. The ''home'' item shows all projects which are owned by you and projects which you have read or write access to. The ''Owned By Me'' item filters the list of projects to show projects which you actually own. The ''Trash'' item filters the list of projects to show projects which you own that are in the trash. Projects that are in the trash do not get deleted, they just aren't visible to other users.

== Creating and Uploading Projects ==

[[File:wp-project-action-buttons.png]]

To create a new empty project press the ''Create Project...'' button. To upload an existing ontology into a new project (either an OWL ontology or an OBO ontology) press the ''Upload Project ...'' button. In both cases a dialog will appear like the one shown below. Enter the name for the project (this need not be unique) and description of the project and press o.k.

[[File:wp-upload-dialog.png]]

== Sharing Project with Collaborators ==

You can share your project with other people so that they can view, comment or edit it. To do this click the ''Share'' link in the top right of the browser window. The sharing settings dialog will appear as shown below.

[[File:wp-sharing-settings.png]]

= Lightweight editing with auto-completion support =

It is now much easier and faster to create content in the new interface of WebProtege that has support for auto-completion.

[[File:WP-classes.png|800px]]

= Collaboration support =

The Changes portlet shows the changes associated to an entity in the ontology. The change tracking provide a full and executable change history.

[[File:WP-changes.png|800px]]

The Project Dashboard provides an overview of the activity in the ontology. The Change Summary portlet shows the changes of the entire ontology, the Watches portlet shows the changes to the watched entities and branches, and the Revisions portlet allows users to download any snapshot in time of the ontology.

[[File:WP-dashboard.png|800px]]

= Viewing and Editing OWL 2 Ontologies =

By default WebProtégé display a simplified user interface that allows you to edit a subset of OWL 2 syntax. In order to view and edit an OWL 2 ontology you can add some OWL 2 portlets to any tab in your project. You can do this by clicking the Add Content button (shown below) on the top right of each tab.

[[File:add-content.png]]

WebProtégé currently contains the following OWL 2 specific portlets:

* '''Conditions''' - Offers a Protégé-4 style view of the class description. Axioms can be added, edited and removed in a similar way that they can in the Protégé-4 class description editor view.

[[File:Conditions-example.png]]

* '''Entity Description''' - shows an extended version of the Manchester Syntax rendering for the selected entity (class, object property, data property, annotation, named individual). For example, the figure below shows the class 'glandular epithelium' being viewed in the [https://github.com/obophenotype/cephalopod-ontology Cephalapod ontology].

[[File:cephalapod-example.png]]

Similarly, the figure below shows the description of object property 'negatively regulates'. The axioms that define 'negatively regulates' are defined in the ro ontology, which is imported by the Cephalapod ontology.

[[File:cephalapod-property-example.png]]

As shown in the Figure below, axiom annotations are shown as indented annotations (a slightly more compact form of the Manchester Syntax).

[[File:axiom-annotations-example.png]]

= Other tabs and portlets =

WebProtégé has a configurable user interface, and each user can customize the layout and save it for future sessions. The user may choose from a list of existing tabs and add portlets dynamically from the user interface. It is also possible to create a new empty tab and add the needed portlets through drag-n-drop. More information on the layout configuration can be found [[WebProtegeLayoutConfig|here]].

= References =

Further documentation and references on WebProtégé can be found [[WebProtege#References|here]].

'''Go back to [[WebProtege|WebProtégé main page]].'''

[[Category:WebProtege documentation]]

File:Axiom-annotations-example.png

2014-03-17T23:06:43Z

Matthewhorridge:

WebProtegeUsersGuide

2014-03-17T22:48:57Z

Matthewhorridge: /* Editing OWL 2 Ontologies */

WebProtégé User Guide

'''WebProtégé''' is an open source, lightweight, web-based ontology editor.

__TOC__

'''Looking for the user guide of the old WebProtege (release 1.0)? [[WebProtege1.0UsersGuide|Here it is]].'''

'''Go back to [[WebProtege|WebProtégé main page]].'''

= Screencasts =

[[File:WP-screencast.png|thumb|70px|left|link=http://www.youtube.com/watch?v=QvURiHVXnQQ]]

You can watch a [http://www.youtube.com/watch?v=QvURiHVXnQQ 15 minutes screencast] that introduces the features of the new WebProtege (creating and uploading ontologies, sharing with collaborators, simplified editing with auto-completion, etc.).

You may also watch a [http://videolectures.net/iswc2013_horridge_webprotege/ 15 minutes presentation] of the simplified user interface of WebProtege and how we came to it that was presented at [http://iswc2013.semanticweb.org/ ISWC 2013].

A more comprehensive [https://stanford.webex.com/stanford/lsr.php?AT=pb&SP=MC&rID=62510447&rKey=13018bdbb414ba08 one-hour long screencast] showing also the OBO editing, and the support for linking to BioPortal is available on the [http://www.bioontology.org/ontology-editing-and-publishing-using-webprotege-and-bioportal NCBO Webinar webpage].

= Home Screen =

When you open http://webprotege.stanford.edu in a browser you should see the list of public projects and various links to create an account or sign in (top right). You can download the ontologies in any publicly available project by clicking the download icon in the table. To open a project click on its name in the Project Name column.

[[File:wp-home-screen.png|800px]]

To create and upload your own projects you need to have a user account and be signed in. If you don't have a user account you can create one using the ''Sign Up for Account'' button. To sign in click the ''Sign In'' link in the top right of the browser window. Enter your user name and password in the dialog that pops up. (You can also sign in with OpenId).

== Nav Bar ==

[[File:Wp-nav-bar.png]]

Once you are signed in you will see a side bar on the left hand side of the screen which offers different categories of projects to view. Clicking on any item in the side bar will filter the list of projects. The ''home'' item shows all projects which are owned by you and projects which you have read or write access to. The ''Owned By Me'' item filters the list of projects to show projects which you actually own. The ''Trash'' item filters the list of projects to show projects which you own that are in the trash. Projects that are in the trash do not get deleted, they just aren't visible to other users.

== Creating and Uploading Projects ==

[[File:wp-project-action-buttons.png]]

To create a new empty project press the ''Create Project...'' button. To upload an existing ontology into a new project (either an OWL ontology or an OBO ontology) press the ''Upload Project ...'' button. In both cases a dialog will appear like the one shown below. Enter the name for the project (this need not be unique) and description of the project and press o.k.

[[File:wp-upload-dialog.png]]

== Sharing Project with Collaborators ==

You can share your project with other people so that they can view, comment or edit it. To do this click the ''Share'' link in the top right of the browser window. The sharing settings dialog will appear as shown below.

[[File:wp-sharing-settings.png]]

= Lightweight editing with auto-completion support =

It is now much easier and faster to create content in the new interface of WebProtege that has support for auto-completion.

[[File:WP-classes.png|800px]]

= Collaboration support =

The Changes portlet shows the changes associated to an entity in the ontology. The change tracking provide a full and executable change history.

[[File:WP-changes.png|800px]]

The Project Dashboard provides an overview of the activity in the ontology. The Change Summary portlet shows the changes of the entire ontology, the Watches portlet shows the changes to the watched entities and branches, and the Revisions portlet allows users to download any snapshot in time of the ontology.

[[File:WP-dashboard.png|800px]]

= Viewing and Editing OWL 2 Ontologies =

By default WebProtégé display a simplified user interface that allows you to edit a subset of OWL 2 syntax. In order to view and edit an OWL 2 ontology you can add some OWL 2 portlets to any tab in your project. You can do this by clicking the Add Content button (shown below) on the top right of each tab.

[[File:add-content.png]]

WebProtégé currently contains the following OWL 2 specific portlets:

* '''Conditions''' - Offers a Protégé-4 style view of the class description. Axioms can be added, edited and removed in a similar way that they can in the Protégé-4 class description editor view.

[[File:Conditions-example.png]]

* '''Entity Description''' - shows an extended version of the Manchester Syntax rendering for the selected entity (class, object property, data property, annotation, named individual). For example, the figure below shows the class 'glandular epithelium' being viewed in the [https://github.com/obophenotype/cephalopod-ontology Cephalapod ontology].

[[File:cephalapod-example.png]]

Similarly, the figure below shows the description of object property 'negatively regulates'. The axioms that define 'negatively regulates' are defined in the ro ontology, which is imported by the Cephalapod ontology.

[[File:cephalapod-property-example.png]]

= Other tabs and portlets =

WebProtégé has a configurable user interface, and each user can customize the layout and save it for future sessions. The user may choose from a list of existing tabs and add portlets dynamically from the user interface. It is also possible to create a new empty tab and add the needed portlets through drag-n-drop. More information on the layout configuration can be found [[WebProtegeLayoutConfig|here]].

= References =

Further documentation and references on WebProtégé can be found [[WebProtege#References|here]].

'''Go back to [[WebProtege|WebProtégé main page]].'''

[[Category:WebProtege documentation]]

WebProtegeUsersGuide

2014-03-17T22:48:35Z

Matthewhorridge:

WebProtégé User Guide

'''WebProtégé''' is an open source, lightweight, web-based ontology editor.

__TOC__

'''Looking for the user guide of the old WebProtege (release 1.0)? [[WebProtege1.0UsersGuide|Here it is]].'''

'''Go back to [[WebProtege|WebProtégé main page]].'''

= Screencasts =

[[File:WP-screencast.png|thumb|70px|left|link=http://www.youtube.com/watch?v=QvURiHVXnQQ]]

You can watch a [http://www.youtube.com/watch?v=QvURiHVXnQQ 15 minutes screencast] that introduces the features of the new WebProtege (creating and uploading ontologies, sharing with collaborators, simplified editing with auto-completion, etc.).

You may also watch a [http://videolectures.net/iswc2013_horridge_webprotege/ 15 minutes presentation] of the simplified user interface of WebProtege and how we came to it that was presented at [http://iswc2013.semanticweb.org/ ISWC 2013].

A more comprehensive [https://stanford.webex.com/stanford/lsr.php?AT=pb&SP=MC&rID=62510447&rKey=13018bdbb414ba08 one-hour long screencast] showing also the OBO editing, and the support for linking to BioPortal is available on the [http://www.bioontology.org/ontology-editing-and-publishing-using-webprotege-and-bioportal NCBO Webinar webpage].

= Home Screen =

When you open http://webprotege.stanford.edu in a browser you should see the list of public projects and various links to create an account or sign in (top right). You can download the ontologies in any publicly available project by clicking the download icon in the table. To open a project click on its name in the Project Name column.

[[File:wp-home-screen.png|800px]]

To create and upload your own projects you need to have a user account and be signed in. If you don't have a user account you can create one using the ''Sign Up for Account'' button. To sign in click the ''Sign In'' link in the top right of the browser window. Enter your user name and password in the dialog that pops up. (You can also sign in with OpenId).

== Nav Bar ==

[[File:Wp-nav-bar.png]]

Once you are signed in you will see a side bar on the left hand side of the screen which offers different categories of projects to view. Clicking on any item in the side bar will filter the list of projects. The ''home'' item shows all projects which are owned by you and projects which you have read or write access to. The ''Owned By Me'' item filters the list of projects to show projects which you actually own. The ''Trash'' item filters the list of projects to show projects which you own that are in the trash. Projects that are in the trash do not get deleted, they just aren't visible to other users.

== Creating and Uploading Projects ==

[[File:wp-project-action-buttons.png]]

To create a new empty project press the ''Create Project...'' button. To upload an existing ontology into a new project (either an OWL ontology or an OBO ontology) press the ''Upload Project ...'' button. In both cases a dialog will appear like the one shown below. Enter the name for the project (this need not be unique) and description of the project and press o.k.

[[File:wp-upload-dialog.png]]

== Sharing Project with Collaborators ==

You can share your project with other people so that they can view, comment or edit it. To do this click the ''Share'' link in the top right of the browser window. The sharing settings dialog will appear as shown below.

[[File:wp-sharing-settings.png]]

= Lightweight editing with auto-completion support =

It is now much easier and faster to create content in the new interface of WebProtege that has support for auto-completion.

[[File:WP-classes.png|800px]]

= Collaboration support =

The Changes portlet shows the changes associated to an entity in the ontology. The change tracking provide a full and executable change history.

[[File:WP-changes.png|800px]]

The Project Dashboard provides an overview of the activity in the ontology. The Change Summary portlet shows the changes of the entire ontology, the Watches portlet shows the changes to the watched entities and branches, and the Revisions portlet allows users to download any snapshot in time of the ontology.

[[File:WP-dashboard.png|800px]]

= Editing OWL 2 Ontologies =

By default WebProtégé display a simplified user interface that allows you to edit a subset of OWL 2 syntax. In order to view and edit an OWL 2 ontology you can add some OWL 2 portlets to any tab in your project. You can do this by clicking the Add Content button (shown below) on the top right of each tab.

[[File:add-content.png]]

WebProtégé currently contains the following OWL 2 specific portlets:

* '''Conditions''' - Offers a Protégé-4 style view of the class description. Axioms can be added, edited and removed in a similar way that they can in the Protégé-4 class description editor view.

[[File:Conditions-example.png]]

* '''Entity Description''' - shows an extended version of the Manchester Syntax rendering for the selected entity (class, object property, data property, annotation, named individual). For example, the figure below shows the class 'glandular epithelium' being viewed in the [https://github.com/obophenotype/cephalopod-ontology Cephalapod ontology].

[[File:cephalapod-example.png]]

Similarly, the figure below shows the description of object property 'negatively regulates'. The axioms that define 'negatively regulates' are defined in the ro ontology, which is imported by the Cephalapod ontology.

[[File:cephalapod-property-example.png]]

= Other tabs and portlets =

WebProtégé has a configurable user interface, and each user can customize the layout and save it for future sessions. The user may choose from a list of existing tabs and add portlets dynamically from the user interface. It is also possible to create a new empty tab and add the needed portlets through drag-n-drop. More information on the layout configuration can be found [[WebProtegeLayoutConfig|here]].

= References =

Further documentation and references on WebProtégé can be found [[WebProtege#References|here]].

'''Go back to [[WebProtege|WebProtégé main page]].'''

[[Category:WebProtege documentation]]

File:Conditions-example.png

2014-03-17T22:47:39Z

Matthewhorridge:

WebProtegeUsersGuide

2014-03-17T22:46:19Z

Matthewhorridge:

WebProtégé User Guide

'''WebProtégé''' is an open source, lightweight, web-based ontology editor.

__TOC__

'''Looking for the user guide of the old WebProtege (release 1.0)? [[WebProtege1.0UsersGuide|Here it is]].'''

'''Go back to [[WebProtege|WebProtégé main page]].'''

= Screencasts =

[[File:WP-screencast.png|thumb|70px|left|link=http://www.youtube.com/watch?v=QvURiHVXnQQ]]

You can watch a [http://www.youtube.com/watch?v=QvURiHVXnQQ 15 minutes screencast] that introduces the features of the new WebProtege (creating and uploading ontologies, sharing with collaborators, simplified editing with auto-completion, etc.).

You may also watch a [http://videolectures.net/iswc2013_horridge_webprotege/ 15 minutes presentation] of the simplified user interface of WebProtege and how we came to it that was presented at [http://iswc2013.semanticweb.org/ ISWC 2013].

A more comprehensive [https://stanford.webex.com/stanford/lsr.php?AT=pb&SP=MC&rID=62510447&rKey=13018bdbb414ba08 one-hour long screencast] showing also the OBO editing, and the support for linking to BioPortal is available on the [http://www.bioontology.org/ontology-editing-and-publishing-using-webprotege-and-bioportal NCBO Webinar webpage].

= Home Screen =

When you open http://webprotege.stanford.edu in a browser you should see the list of public projects and various links to create an account or sign in (top right). You can download the ontologies in any publicly available project by clicking the download icon in the table. To open a project click on its name in the Project Name column.

[[File:wp-home-screen.png|800px]]

To create and upload your own projects you need to have a user account and be signed in. If you don't have a user account you can create one using the ''Sign Up for Account'' button. To sign in click the ''Sign In'' link in the top right of the browser window. Enter your user name and password in the dialog that pops up. (You can also sign in with OpenId).

== Nav Bar ==

[[File:Wp-nav-bar.png]]

Once you are signed in you will see a side bar on the left hand side of the screen which offers different categories of projects to view. Clicking on any item in the side bar will filter the list of projects. The ''home'' item shows all projects which are owned by you and projects which you have read or write access to. The ''Owned By Me'' item filters the list of projects to show projects which you actually own. The ''Trash'' item filters the list of projects to show projects which you own that are in the trash. Projects that are in the trash do not get deleted, they just aren't visible to other users.

== Creating and Uploading Projects ==

[[File:wp-project-action-buttons.png]]

To create a new empty project press the ''Create Project...'' button. To upload an existing ontology into a new project (either an OWL ontology or an OBO ontology) press the ''Upload Project ...'' button. In both cases a dialog will appear like the one shown below. Enter the name for the project (this need not be unique) and description of the project and press o.k.

[[File:wp-upload-dialog.png]]

== Sharing Project with Collaborators ==

You can share your project with other people so that they can view, comment or edit it. To do this click the ''Share'' link in the top right of the browser window. The sharing settings dialog will appear as shown below.

[[File:wp-sharing-settings.png]]

= Lightweight editing with auto-completion support =

It is now much easier and faster to create content in the new interface of WebProtege that has support for auto-completion.

[[File:WP-classes.png|800px]]

= Collaboration support =

The Changes portlet shows the changes associated to an entity in the ontology. The change tracking provide a full and executable change history.

[[File:WP-changes.png|800px]]

The Project Dashboard provides an overview of the activity in the ontology. The Change Summary portlet shows the changes of the entire ontology, the Watches portlet shows the changes to the watched entities and branches, and the Revisions portlet allows users to download any snapshot in time of the ontology.

[[File:WP-dashboard.png|800px]]

= Editing OWL 2 Ontologies =

By default WebProtégé display a simplified user interface that allows you to edit a subset of OWL 2 syntax. In order to view and edit an OWL 2 ontology you can add some OWL 2 portlets to any tab in your project. You can do this by clicking the Add Content button (shown below) on the top right of each tab.

[[File:add-content.png]]

WebProtégé currently contains the following OWL 2 specific portlets:

* '''Conditions''' - Offers a Protégé-4 style view of the class description. Axioms can be added, edited and removed in a similar way that they can in the Protégé-4 class description editor view.

* '''Entity Description''' - shows an extended version of the Manchester Syntax rendering for the selected entity (class, object property, data property, annotation, named individual). For example, the figure below shows the class 'glandular epithelium' being viewed in the [https://github.com/obophenotype/cephalopod-ontology Cephalapod ontology].

[[File:cephalapod-example.png]]

Similarly, the figure below shows the description of object property 'negatively regulates'. The axioms that define 'negatively regulates' are defined in the ro ontology, which is imported by the Cephalapod ontology.

[[File:cephalapod-property-example.png]]

= Other tabs and portlets =

WebProtégé has a configurable user interface, and each user can customize the layout and save it for future sessions. The user may choose from a list of existing tabs and add portlets dynamically from the user interface. It is also possible to create a new empty tab and add the needed portlets through drag-n-drop. More information on the layout configuration can be found [[WebProtegeLayoutConfig|here]].

= References =

Further documentation and references on WebProtégé can be found [[WebProtege#References|here]].

'''Go back to [[WebProtege|WebProtégé main page]].'''

[[Category:WebProtege documentation]]

File:Add-content.png

2014-03-17T22:45:02Z

Matthewhorridge:

WebProtegeUsersGuide

2014-03-17T22:44:32Z

Matthewhorridge:

WebProtégé User Guide

'''WebProtégé''' is an open source, lightweight, web-based ontology editor.

__TOC__

'''Looking for the user guide of the old WebProtege (release 1.0)? [[WebProtege1.0UsersGuide|Here it is]].'''

'''Go back to [[WebProtege|WebProtégé main page]].'''

= Screencasts =

[[File:WP-screencast.png|thumb|70px|left|link=http://www.youtube.com/watch?v=QvURiHVXnQQ]]

You can watch a [http://www.youtube.com/watch?v=QvURiHVXnQQ 15 minutes screencast] that introduces the features of the new WebProtege (creating and uploading ontologies, sharing with collaborators, simplified editing with auto-completion, etc.).

You may also watch a [http://videolectures.net/iswc2013_horridge_webprotege/ 15 minutes presentation] of the simplified user interface of WebProtege and how we came to it that was presented at [http://iswc2013.semanticweb.org/ ISWC 2013].

A more comprehensive [https://stanford.webex.com/stanford/lsr.php?AT=pb&SP=MC&rID=62510447&rKey=13018bdbb414ba08 one-hour long screencast] showing also the OBO editing, and the support for linking to BioPortal is available on the [http://www.bioontology.org/ontology-editing-and-publishing-using-webprotege-and-bioportal NCBO Webinar webpage].

= Home Screen =

When you open http://webprotege.stanford.edu in a browser you should see the list of public projects and various links to create an account or sign in (top right). You can download the ontologies in any publicly available project by clicking the download icon in the table. To open a project click on its name in the Project Name column.

[[File:wp-home-screen.png|800px]]

To create and upload your own projects you need to have a user account and be signed in. If you don't have a user account you can create one using the ''Sign Up for Account'' button. To sign in click the ''Sign In'' link in the top right of the browser window. Enter your user name and password in the dialog that pops up. (You can also sign in with OpenId).

== Nav Bar ==

[[File:Wp-nav-bar.png]]

Once you are signed in you will see a side bar on the left hand side of the screen which offers different categories of projects to view. Clicking on any item in the side bar will filter the list of projects. The ''home'' item shows all projects which are owned by you and projects which you have read or write access to. The ''Owned By Me'' item filters the list of projects to show projects which you actually own. The ''Trash'' item filters the list of projects to show projects which you own that are in the trash. Projects that are in the trash do not get deleted, they just aren't visible to other users.

== Creating and Uploading Projects ==

[[File:wp-project-action-buttons.png]]

To create a new empty project press the ''Create Project...'' button. To upload an existing ontology into a new project (either an OWL ontology or an OBO ontology) press the ''Upload Project ...'' button. In both cases a dialog will appear like the one shown below. Enter the name for the project (this need not be unique) and description of the project and press o.k.

[[File:wp-upload-dialog.png]]

== Sharing Project with Collaborators ==

You can share your project with other people so that they can view, comment or edit it. To do this click the ''Share'' link in the top right of the browser window. The sharing settings dialog will appear as shown below.

[[File:wp-sharing-settings.png]]

= Lightweight editing with auto-completion support =

It is now much easier and faster to create content in the new interface of WebProtege that has support for auto-completion.

[[File:WP-classes.png|800px]]

= Collaboration support =

The Changes portlet shows the changes associated to an entity in the ontology. The change tracking provide a full and executable change history.

[[File:WP-changes.png|800px]]

The Project Dashboard provides an overview of the activity in the ontology. The Change Summary portlet shows the changes of the entire ontology, the Watches portlet shows the changes to the watched entities and branches, and the Revisions portlet allows users to download any snapshot in time of the ontology.

[[File:WP-dashboard.png|800px]]

= Editing OWL 2 Ontologies =

By default WebProtégé display a simplified user interface that allows you to edit a subset of OWL 2 syntax. In order to view and edit an OWL 2 ontology you can add some OWL 2 portlets to any tab in your project. WebProtégé currently contains the following OWL 2 specific portlets:

* '''Conditions''' - Offers a Protégé-4 style view of the class description. Axioms can be added, edited and removed in a similar way that they can in the Protégé-4 class description editor view.

* '''Entity Description''' - shows an extended version of the Manchester Syntax rendering for the selected entity (class, object property, data property, annotation, named individual). For example, the figure below shows the class 'glandular epithelium' being viewed in the [https://github.com/obophenotype/cephalopod-ontology Cephalapod ontology].

[[File:cephalapod-example.png]]

Similarly, the figure below shows the description of object property 'negatively regulates'. The axioms that define 'negatively regulates' are defined in the ro ontology, which is imported by the Cephalapod ontology.

[[File:cephalapod-property-example.png]]

= Other tabs and portlets =

WebProtégé has a configurable user interface, and each user can customize the layout and save it for future sessions. The user may choose from a list of existing tabs and add portlets dynamically from the user interface. It is also possible to create a new empty tab and add the needed portlets through drag-n-drop. More information on the layout configuration can be found [[WebProtegeLayoutConfig|here]].

= References =

Further documentation and references on WebProtégé can be found [[WebProtege#References|here]].

'''Go back to [[WebProtege|WebProtégé main page]].'''

[[Category:WebProtege documentation]]

File:Cephalapod-property-example.png

2014-03-17T22:36:43Z

Matthewhorridge:

File:Cephalapod-example.png

2014-03-17T22:36:21Z

Matthewhorridge:

WebProtege

2013-09-12T00:26:38Z

Matthewhorridge:

WebProtégé 

'''WebProtégé is an open source, lightweight, web-based ontology editor. WebProtégé provides a friendly and highly configurable user interface that can be adapted for the use of domain experts. It has support for form-based editing and full-fledged collaboration. ''' 

[[File:WP-classes.png|thumb|400px|right|text-bottom|The new WebProtege with simplified editing and improved collaboration support]]

<div style="background: #FDF3E7; border: 1px solid #AE5B08; padding: 10px 15px 10px 20px; margin: 30px 430px 0 0; ">

'''LATEST ACTIVITY:'''

'''11th September 2013:''' [https://github.com/protegeproject/webprotege/releases/download/106/webprotege-build-106.zip WebProtege build 106] is available.

'''12th August 2013:''' WebProtege source code is now on [http://github.com/protegeproject/webprotege GitHub].

'''24th July 2013:''' [[WebProtegeAdminGuide|WebProtege build 105]] is available. Read more in the [[WebProtegeReleaseNotes|release notes]].

'''25th April 2013:''' '''The new WebProtege is here!'''
<ul>
<li>Upload your ontologies to the new WebProtege server: http://webprotege.stanford.edu </li>
<li>New exciting features: simplified editing, improved collaboration support, OWL-API based, etc. Read more in the [[WebProtegeReleaseNotes|release notes]].</li>
<li>You may also [[WebProtegeAdminGuide|download and install]] the new WebProtege</li>
</ul>

'''25th April 2013:''' The final release of [[WebProtegeAdminGuide|WebProtege release 1.0]] now available!
<ul>
<li>The WebProtege 1.0 demo server has been moved to: http://wp-obs.stanford.edu </li>
<li>Read how to [[MigrateOntologiesFromWP1|move]] your ontologies to the new WebProtege server available on http://webprotege.stanford.edu</li>
<li>We don't plan to further develop WebProtege 1.0, so please consider upgrading to the new WebProtege (see above). See [[WebProtegeReleaseNotes|release notes]].</li>
</ul>

'''10th Oct 2012:''' WebProtege Webinar
<ul>
<li>See the recorded [http://www.bioontology.org/ontology-editing-and-publishing-using-webprotege-and-bioportal NCBO webcast] on publishing and editing OWL2 and OBO ontologies with the new WebProtege </li>
</ul>

</div> 

__NOTOC__

== Documentation ==

=== [[WebProtegeUsersGuide|User's Guide]] ===
A short [[WebProtegeUsersGuide|user guide]] with screencasts and screenshots describing the main user interface elements in WebProtégé.

=== [[WebProtegeAdminGuide|Download and Install - Administrator's Guide]] ===
A [[WebProtegeAdminGuide|step-by-step guide]] for site administrators who want to download and install WebProtégé.

=== [[WebProtegeDevelopersGuide|Developer's Guide]] ===
A [[WebProtegeDevelopersGuide|guide]] for developers who want to compile and run WebProtégé from an IDE.

== About WebProtégé ==
WebProtégé is being actively developed by the [http://protege.stanford.edu/aboutus/aboutus.html Protégé team] at the [[Affiliated with::Stanford Center for Biomedical Informatics Research]].

== References ==

* A WebProtege paper describing its architecture, features and use in real-world cases is published in the Semantic Web Journal, and is available [http://www.semantic-web-journal.net/content/webprot%C3%A9g%C3%A9-distributed-ontology-editor-and-knowledge-acquisition-tool-web here].

* Several papers describing the use of WebProtégé in real use cases can be found [http://bmir.stanford.edu/publications/by_author.php/tania_tudorache here].

== How to cite WebProtégé ==

T. Tudorache, C.I. Nyulas, N.F. Noy, M.A. Musen. WebProtégé: A Collaborative Ontology Editor and Knowledge Acquisition Tool for the Web, Semantic Web Journal, IOS Press, 2011

Online version available [http://www.semantic-web-journal.net/content/webprot%C3%A9g%C3%A9-distributed-ontology-editor-and-knowledge-acquisition-tool-web here].

== Contact Us ==
If you have questions or comments, please post them on the [https://mailman.stanford.edu/mailman/listinfo/webprotege-feedback WebProtégé mailing list]. 

[[Category:Application]]
[[Category:WebProtege documentation]]

WebProtege

2013-08-12T22:18:53Z

Matthewhorridge:

WebProtégé 

'''WebProtégé is an open source, lightweight, web-based ontology editor. WebProtégé provides a friendly and highly configurable user interface that can be adapted for the use of domain experts. It has support for form-based editing and full-fledged collaboration. ''' 

[[File:WP-classes.png|thumb|400px|right|text-bottom|The new WebProtege with simplified editing and improved collaboration support]]

<div style="background: #FDF3E7; border: 1px solid #AE5B08; padding: 10px 15px 10px 20px; margin: 30px 430px 0 0; ">

'''LATEST ACTIVITY:'''

'''12th August 2013:''' WebProtege source code is now on [http://github.com/protegeproject/webprotege GitHub].

'''24th July 2013:''' [[WebProtegeAdminGuide|WebProtege build 105]] is available. Read more in the [[WebProtegeReleaseNotes|release notes]].

'''5th July 2013:''' [[WebProtegeAdminGuide|WebProtege build 104]] is available. Read more in the [[WebProtegeReleaseNotes|release notes]].

'''20th May 2013:''' [[WebProtegeAdminGuide|WebProtege build 103]] is available. Read more in the [[WebProtegeReleaseNotes|release notes]].

'''25th April 2013:''' '''The new WebProtege is here!'''
<ul>
<li>Upload your ontologies to the new WebProtege server: http://webprotege.stanford.edu </li>
<li>New exciting features: simplified editing, improved collaboration support, OWL-API based, etc. Read more in the [[WebProtegeReleaseNotes|release notes]].</li>
<li>You may also [[WebProtegeAdminGuide|download and install]] the new WebProtege</li>
</ul>

'''25th April 2013:''' The final release of [[WebProtegeAdminGuide|WebProtege release 1.0]] now available!
<ul>
<li>The WebProtege 1.0 demo server has been moved to: http://wp-obs.stanford.edu </li>
<li>Read how to [[MigrateOntologiesFromWP1|move]] your ontologies to the new WebProtege server available on http://webprotege.stanford.edu</li>
<li>We don't plan to further develop WebProtege 1.0, so please consider upgrading to the new WebProtege (see above). See [[WebProtegeReleaseNotes|release notes]].</li>
</ul>

'''10th Oct 2012:''' WebProtege Webinar
<ul>
<li>See the recorded [http://www.bioontology.org/ontology-editing-and-publishing-using-webprotege-and-bioportal NCBO webcast] on publishing and editing OWL2 and OBO ontologies with the new WebProtege </li>
</ul>

</div> 

__NOTOC__

== Documentation ==

=== [[WebProtegeUsersGuide|User's Guide]] ===
A short [[WebProtegeUsersGuide|user guide]] with screencasts and screenshots describing the main user interface elements in WebProtégé.

=== [[WebProtegeAdminGuide|Download and Install - Administrator's Guide]] ===
A [[WebProtegeAdminGuide|step-by-step guide]] for site administrators who want to download and install WebProtégé.

=== [[WebProtegeDevelopersGuide|Developer's Guide]] ===
A [[WebProtegeDevelopersGuide|guide]] for developers who want to compile and run WebProtégé from an IDE.

== About WebProtégé ==
WebProtégé is being actively developed by the [http://protege.stanford.edu/aboutus/aboutus.html Protégé team] at the [[Affiliated with::Stanford Center for Biomedical Informatics Research]].

== References ==

* A WebProtege paper describing its architecture, features and use in real-world cases is published in the Semantic Web Journal, and is available [http://www.semantic-web-journal.net/content/webprot%C3%A9g%C3%A9-distributed-ontology-editor-and-knowledge-acquisition-tool-web here].

* Several papers describing the use of WebProtégé in real use cases can be found [http://bmir.stanford.edu/publications/by_author.php/tania_tudorache here].

== How to cite WebProtégé ==

T. Tudorache, C.I. Nyulas, N.F. Noy, M.A. Musen. WebProtégé: A Collaborative Ontology Editor and Knowledge Acquisition Tool for the Web, Semantic Web Journal, IOS Press, 2011

Online version available [http://www.semantic-web-journal.net/content/webprot%C3%A9g%C3%A9-distributed-ontology-editor-and-knowledge-acquisition-tool-web here].

== Contact Us ==
If you have questions or comments, please post them on the [https://mailman.stanford.edu/mailman/listinfo/webprotege-feedback WebProtégé mailing list]. 

[[Category:Application]]
[[Category:WebProtege documentation]]

WebProtege

2013-07-08T18:42:30Z

Matthewhorridge:

WebProtégé 

'''WebProtégé is an open source, lightweight, web-based ontology editor. WebProtégé provides a friendly and highly configurable user interface that can be adapted for the use of domain experts. It has support for form-based editing and full-fledged collaboration. ''' 

[[File:WP-classes.png|thumb|400px|right|text-bottom|The new WebProtege with simplified editing and improved collaboration support]]

<div style="background: #FDF3E7; border: 1px solid #AE5B08; padding: 10px 15px 10px 20px; margin: 30px 430px 0 0; ">

'''LATEST ACTIVITY:'''

'''5th July 2013:''' [[WebProtegeAdminGuide|WebProtege build 104]] is available. Read more in the [[WebProtegeReleaseNotes|release notes]].

'''20th May 2013:''' [[WebProtegeAdminGuide|WebProtege build 103]] is available. Read more in the [[WebProtegeReleaseNotes|release notes]].

'''25th April 2013:''' '''The new WebProtege is here!'''
<ul>
<li>Upload your ontologies to the new WebProtege server: http://webprotege.stanford.edu </li>
<li>New exciting features: simplified editing, improved collaboration support, OWL-API based, etc. Read more in the [[WebProtegeReleaseNotes|release notes]].</li>
<li>You may also [[WebProtegeAdminGuide|download and install]] the new WebProtege</li>
</ul>

'''25th April 2013:''' The final release of [[WebProtegeAdminGuide|WebProtege release 1.0]] now available!
<ul>
<li>The WebProtege 1.0 demo server has been moved to: http://wp-obs.stanford.edu </li>
<li>Read how to [[MigrateOntologiesFromWP1|move]] your ontologies to the new WebProtege server available on http://webprotege.stanford.edu</li>
<li>We don't plan to further develop WebProtege 1.0, so please consider upgrading to the new WebProtege (see above). See [[WebProtegeReleaseNotes|release notes]].</li>
</ul>

'''10th Oct 2012:''' WebProtege Webinar
<ul>
<li>See the recorded [http://www.bioontology.org/ontology-editing-and-publishing-using-webprotege-and-bioportal NCBO webcast] on publishing and editing OWL2 and OBO ontologies with the new WebProtege </li>
</ul>

</div> 

__NOTOC__

== Documentation ==

=== [[WebProtegeUsersGuide|User's Guide]] ===
A short [[WebProtegeUsersGuide|user guide]] with screencasts and screenshots describing the main user interface elements in WebProtégé.

=== [[WebProtegeAdminGuide|Download and Install - Administrator's Guide]] ===
A [[WebProtegeAdminGuide|step-by-step guide]] for site administrators who want to download and install WebProtégé.

=== [[WebProtegeDevelopersGuide|Developer's Guide]] ===
A [[WebProtegeDevelopersGuide|guide]] for developers who want to compile and run WebProtégé from an IDE.

== About WebProtégé ==
WebProtégé is being actively developed by the [http://protege.stanford.edu/aboutus/aboutus.html Protégé team] at the [[Affiliated with::Stanford Center for Biomedical Informatics Research]].

== References ==

* A WebProtege paper describing its architecture, features and use in real-world cases is published in the Semantic Web Journal, and is available [http://www.semantic-web-journal.net/content/webprot%C3%A9g%C3%A9-distributed-ontology-editor-and-knowledge-acquisition-tool-web here].

* Several papers describing the use of WebProtégé in real use cases can be found [http://bmir.stanford.edu/publications/by_author.php/tania_tudorache here].

== How to cite WebProtégé ==

T. Tudorache, C.I. Nyulas, N.F. Noy, M.A. Musen. WebProtégé: A Collaborative Ontology Editor and Knowledge Acquisition Tool for the Web, Semantic Web Journal, IOS Press, 2011

Online version available [http://www.semantic-web-journal.net/content/webprot%C3%A9g%C3%A9-distributed-ontology-editor-and-knowledge-acquisition-tool-web here].

== Contact Us ==
If you have questions or comments, please post them on the [https://mailman.stanford.edu/mailman/listinfo/webprotege-feedback WebProtégé mailing list]. 

[[Category:Application]]
[[Category:WebProtege documentation]]

WebProtege

2013-07-08T18:41:47Z

Matthewhorridge:

WebProtégé 

'''WebProtégé is an open source, lightweight, web-based ontology editor. WebProtégé provides a friendly and highly configurable user interface that can be adapted for the use of domain experts. It has support for form-based editing and full-fledged collaboration. ''' 

[[File:WP-classes.png|thumb|400px|right|text-bottom|The new WebProtege with simplified editing and improved collaboration support]]

<div style="background: #FDF3E7; border: 1px solid #AE5B08; padding: 10px 15px 10px 20px; margin: 30px 430px 0 0; ">

'''LATEST ACTIVITY:'''

'''5th July 2013:''' [[WebProtegeAdminGuide|WebProtege build 104]] is available. Read more in the [[WebProtegeReleaseNotes|release notes]].

'''20 May 2013:''' [[WebProtegeAdminGuide|WebProtege build 103]] is available. Read more in the [[WebProtegeReleaseNotes|release notes]].

'''25 April 2013:''' '''The new WebProtege is here!'''
<ul>
<li>Upload your ontologies to the new WebProtege server: http://webprotege.stanford.edu </li>
<li>New exciting features: simplified editing, improved collaboration support, OWL-API based, etc. Read more in the [[WebProtegeReleaseNotes|release notes]].</li>
<li>You may also [[WebProtegeAdminGuide|download and install]] the new WebProtege</li>
</ul>

'''25 April 2013:''' The final release of [[WebProtegeAdminGuide|WebProtege release 1.0]] now available!
<ul>
<li>The WebProtege 1.0 demo server has been moved to: http://wp-obs.stanford.edu </li>
<li>Read how to [[MigrateOntologiesFromWP1|move]] your ontologies to the new WebProtege server available on http://webprotege.stanford.edu</li>
<li>We don't plan to further develop WebProtege 1.0, so please consider upgrading to the new WebProtege (see above). See [[WebProtegeReleaseNotes|release notes]].</li>
</ul>

'''10 Oct 2012:''' WebProtege Webinar
<ul>
<li>See the recorded [http://www.bioontology.org/ontology-editing-and-publishing-using-webprotege-and-bioportal NCBO webcast] on publishing and editing OWL2 and OBO ontologies with the new WebProtege </li>
</ul>

</div> 

__NOTOC__

== Documentation ==

=== [[WebProtegeUsersGuide|User's Guide]] ===
A short [[WebProtegeUsersGuide|user guide]] with screencasts and screenshots describing the main user interface elements in WebProtégé.

=== [[WebProtegeAdminGuide|Download and Install - Administrator's Guide]] ===
A [[WebProtegeAdminGuide|step-by-step guide]] for site administrators who want to download and install WebProtégé.

=== [[WebProtegeDevelopersGuide|Developer's Guide]] ===
A [[WebProtegeDevelopersGuide|guide]] for developers who want to compile and run WebProtégé from an IDE.

== About WebProtégé ==
WebProtégé is being actively developed by the [http://protege.stanford.edu/aboutus/aboutus.html Protégé team] at the [[Affiliated with::Stanford Center for Biomedical Informatics Research]].

== References ==

* A WebProtege paper describing its architecture, features and use in real-world cases is published in the Semantic Web Journal, and is available [http://www.semantic-web-journal.net/content/webprot%C3%A9g%C3%A9-distributed-ontology-editor-and-knowledge-acquisition-tool-web here].

* Several papers describing the use of WebProtégé in real use cases can be found [http://bmir.stanford.edu/publications/by_author.php/tania_tudorache here].

== How to cite WebProtégé ==

T. Tudorache, C.I. Nyulas, N.F. Noy, M.A. Musen. WebProtégé: A Collaborative Ontology Editor and Knowledge Acquisition Tool for the Web, Semantic Web Journal, IOS Press, 2011

Online version available [http://www.semantic-web-journal.net/content/webprot%C3%A9g%C3%A9-distributed-ontology-editor-and-knowledge-acquisition-tool-web here].

== Contact Us ==
If you have questions or comments, please post them on the [https://mailman.stanford.edu/mailman/listinfo/webprotege-feedback WebProtégé mailing list]. 

[[Category:Application]]
[[Category:WebProtege documentation]]

WebProtegeReleaseNotes

2013-07-08T18:36:21Z

Matthewhorridge:

WebProtege Release Notes 

__TOC__

'''Go back to the [[WebProtege|WebProtege main page]].

== 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 <code>default-ui-configuration-data</code> 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) ==

[[File:WP-classes.png|thumb|400px|right]]

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 [http://owlapi.sourceforge.net/ 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 '''[[WebProtegeAdminGuide|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 [[MigrateOntologiesFromWP1|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 [[MigrateOntologiesFromWP1|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 [https://mailman.stanford.edu/mailman/listinfo/webprotege-feedback 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 [https://mailman.stanford.edu/mailman/listinfo/webprotege-feedback 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|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 [[WebProtege1.0AdminGuide|WebProtege 1.0 Administrator's Guide]].

== WebProtege Beta Series ==

=== February 7, 2013 ===

'''Take a look at the recorded [http://www.bioontology.org/ontology-editing-and-publishing-using-webprotege-and-bioportal 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/ 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).

[[Image:WebProtege_2.0_Beta.png]]

=== January 12, 2013 ===

[[Image:WebProtege_2.0_Beta.png|thumb|400px|right|Screenshot of OBO-specific widgets - new in 2.0 beta!]]

We are very excited to announce [[WebProtege|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/ http://webprotege-beta.stanford.edu/]''' 

''' Release Highlights '''

''This section describes changes relative to WebProtege 0.5''

<ul>
<li>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.</li>
<li>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.</li>
<li>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).</li>
</ul>

=== June 4, 2012 ===

<ul>
<li>Initial software release to demo server [http://webprotege-beta.stanford.edu/ http://webprotege-beta.stanford.edu/].</li>
</ul>

== 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 <code>edu.stanford.bmir.protege.web.client.ui.util.SelectionUtil</code> class for the selection of classes and individuals in the ontology.

=== Beta Build 500 - May 13, 2011 ===

* Compatible with [http://protege.stanford.edu/download/protege/3.4/installanywhere/Web_Installers/ Protege 3.4.6] (for the external server mode), [http://google-web-toolkit.googlecode.com/files/gwt-2.2.0.zip 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 [[Protege_Client_Server_Tutorial_Configuration|metaproject]].

* Users can now [[WebProtegeOpenId|'''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 [[WebProtegeWatches|'''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 [[WebProtegeNotifications|'''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 [[WebProtegeLayoutConfig|'''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 [[PropertyFormPortlet|'''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 [[PropertyFormPortlet|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 [http://bioportal.bioontology.org 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 [[WebProtegeDevelopersGuide|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) ====

<ul>
<li>Upgraded to [http://code.google.com/webtoolkit/releases/release-notes-1.7.0.html#Release_Notes_Current GWT 1.7].</li>

<li style="padding-top:5px;">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 [[WebProtegeAdminGuide|Administrator's Guide]] for updated instructions. Developers should look at the [[WebProtegeDevelopersGuide|Developer's Guide]] - the setup for compiling and running WebProtege has been greatly simplified thanks to the Google Plugin for Eclipse.

<li style="padding-top:5px;">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 <code><your-servlet-container>/webprotege</code> 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:
<pre>
# 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
</pre>

Values of properties listed above should be changed to match your custom WebProtege installation.
</li>

<li style="padding-top:5px;">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.</li>

<li style="padding-top:5px;">Users can now open multiple ontologies in WebProtege. Each ontology is displayed in a separate tab.</li>
</ul>

==== Other Changes ====

<ul>
<li>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.</li>

<li style="padding-top:5px;">Added more support for editing; users with write permission on a particular project are now able to:
<ul>
<li>Create and delete classes in the Classes tab</li>
<li>Create and delete properties in the Properties tab</li>
<li>Edit string property values in the Properties portlet</li>
<li>Edit the domain and range of properties in the Properties tab</li>
</ul>
</li>

<li style="padding-top:5px;">New portlet is available; the BioPortal Search portlet allows users to search for terms in the [http://bioontology.org/tools/portal/bioportal.html BioPortal repository] and import the terms as references in WebProtege ontologies.</li>

<li style="padding-top:5px;">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: 
<ul>
<li>textfield</li>
<li>textarea</li>
<li>HTML pane</li>
<li>instance grid (similar to the InstanceTable in Protege standalone)</li>
<li>external reference</li>
<li>multifield</li>
<li>combo-box; not working yet... :)</li>.
</ul>
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.</li>

<li style="padding-top:5px;">The Properties tab now shows different icons for the different property types.</li>

<li style="padding-top:5px;">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".</li>

<li style="padding-top:5px;">Web links are now opened in a new browser window.</li>

<li style="padding-top:5px;">Better logging in the Servlet container and Protege server logs if something goes wrong.</li>

<li style="padding-top:5px;">If running in external server mode, WebProtege will cleanly handle situations in which the Protege server becomes unavailable.</li>

<li style="padding-top:5px;">RPC calls are now available for creating/deleting classes and setting property values.</li>

<li style="padding-top:5px;">Support for multiple change events. Portlets can register listeners for class and property creation, deletion, and for property value changed.</li>
</ul>

=== 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

[[Category:WebProtege documentation]]

WebProtegeUsersGuide

2013-04-25T23:33:48Z

Matthewhorridge:

WebProtégé User Guide

'''WebProtégé''' is an open source, lightweight, web-based ontology editor.

__TOC__

'''Go back to [[WebProtege|WebProtégé main page]].'''

'''Looking for the user guide of the old WebProtege (release 1.0)? [[WebProtege1.0UsersGuide|Here]] it is.'''

= Home Screen =

When you open webprotege.stanford.edu in a browser you should see the list of public projects and various links to create an account or sign in (top right). You can download the ontologies in any publicly available project by clicking the download icon in the table. To open a project click on its name in the Project Name column.

[[File:wp-home-screen.png]]

To create and upload your own projects you need to have a user account and be signed in. If you don't have a user account you can create one using the "Sign Up for Account" button. To sign in click the "Sign In" link in the top right of the browser window. Enter your user name and password in the dialog that pops up. (You can also sign in with OpenId).

== Nav Bar ==

[[File:Wp-nav-bar.png]]

Once you are signed in you will see a side bar on the left hand side of the screen which offers different categories of projects to view. Clicking on any item in the side bar will filter the list of projects. The ''home'' item shows all projects which are owned by you and projects which you have read or write access to. The ''Owned By Me'' item filters the list of projects to show projects which you actually own. The ''Trash'' item filters the list of projects to show projects which you own that are in the trash. Projects that are in the trash do not get deleted, they just aren't visible to other users.

== Creating and Uploading Projects ==

[[File:wp-project-action-buttons.png]]

To create a new empty project press the ''Create Project...'' button. To upload an existing ontology into a new project (either an OWL ontology or an OBO ontology) press the ''Upload Project ...'' button. In both cases a dialog will appear like the one shown below. Enter the name for the project (this need not be unique) and description of the project and press o.k.

[[File:wp-upload-dialog.png]]

== Sharing Project with Collaborators ==

You can share your project with other people so that they can view, comment or edit it. To do this click the ''Share'' link in the top right of the browser window. The sharing settings dialog will appear as shown below.

[[File:wp-sharing-settings.png]]

=== Other tabs and portlets ===

WebProtégé has a configurable user interface, and each user can customize the layout and save it for future sessions. The user may choose from a list of existing tabs and add portlets dynamically from the user interface. It is also possible to create a new empty tab and add the needed portlets through drag-n-drop. More information on the layout configuration can be found [[WebProtegeLayoutConfig|here]].

== References ==

Further documentation and references on WebProtégé can be found [[WebProtege#References|here]].

'''Go back to [[WebProtege|WebProtégé main page]].'''

[[Category:WebProtege documentation]]

WebProtegeUsersGuide

2013-04-25T23:32:12Z

Matthewhorridge:

WebProtégé User Guide

'''WebProtégé''' is an open source, lightweight, web-based ontology editor.

__TOC__

'''Go back to [[WebProtege|WebProtégé main page]].'''

'''Looking for the user guide of the old WebProtege (release 1.0)? [[WebProtege1.0UsersGuide|Here]] it is.'''

= Home Screen =

When you open webprotege.stanford.edu in a browser you should see the list of public projects and various links to create an account or sign in (top right). You can download the ontologies in any publicly available project by clicking the download icon in the table. To open a project click on its name in the Project Name column.

[[File:wp-home-screen.png]]

To create and upload your own projects you need to have a user account and be signed in. If you don't have a user account you can create one using the "Sign Up for Account" button. To sign in click the "Sign In" link in the top right of the browser window. Enter your user name and password in the dialog that pops up. (You can also sign in with OpenId).

== Nav Bar ==

[[File:Wp-nav-bar.png]]

Once you are signed in you will see a side bar on the left hand side of the screen which offers different categories of projects to view. Clicking on any item in the side bar will filter the list of projects. The ''home'' item shows all projects which are owned by you and projects which you have read or write access to. The ''Owned By Me'' item filters the list of projects to show projects which you actually own. The ''Trash'' item filters the list of projects to show projects which you own that are in the trash. Projects that are in the trash do not get deleted, they just aren't visible to other users.

== Creating and Uploading Projects ==

[[File:wp-project-action-buttons.png]]

To create a new empty project press the ''Create Project...'' button. To upload an existing ontology into a new project (either an OWL ontology or an OBO ontology) press the ''Upload Project ...'' button. In both cases a dialog will appear like the one shown below. Enter the name for the project (this need not be unique) and description of the project and press o.k.

[[File:wp-upload-dialog.png]]

== Sharing Project with Collaborators ==

[[File:wp-sharing-settings]]

=== Other tabs and portlets ===

WebProtégé has a configurable user interface, and each user can customize the layout and save it for future sessions. The user may choose from a list of existing tabs and add portlets dynamically from the user interface. It is also possible to create a new empty tab and add the needed portlets through drag-n-drop. More information on the layout configuration can be found [[WebProtegeLayoutConfig|here]].

== References ==

Further documentation and references on WebProtégé can be found [[WebProtege#References|here]].

'''Go back to [[WebProtege|WebProtégé main page]].'''

[[Category:WebProtege documentation]]

File:Wp-sharing-settings.png

2013-04-25T23:31:31Z

Matthewhorridge:

WebProtegeUsersGuide

2013-04-25T23:30:05Z

Matthewhorridge:

WebProtégé User Guide

'''WebProtégé''' is an open source, lightweight, web-based ontology editor.

__TOC__

'''Go back to [[WebProtege|WebProtégé main page]].'''

'''Looking for the user guide of the old WebProtege (release 1.0)? [[WebProtege1.0UsersGuide|Here]] it is.'''

= Home Screen =

When you open webprotege.stanford.edu in a browser you should see the list of public projects and various links to create an account or sign in (top right). You can download the ontologies in any publicly available project by clicking the download icon in the table. To open a project click on its name in the Project Name column.

[[File:wp-home-screen.png]]

To create and upload your own projects you need to have a user account and be signed in. If you don't have a user account you can create one using the "Sign Up for Account" button. To sign in click the "Sign In" link in the top right of the browser window. Enter your user name and password in the dialog that pops up. (You can also sign in with OpenId).

== Nav Bar ==

[[File:Wp-nav-bar.png]]

Once you are signed in you will see a side bar on the left hand side of the screen which offers different categories of projects to view. Clicking on any item in the side bar will filter the list of projects. The ''home'' item shows all projects which are owned by you and projects which you have read or write access to. The ''Owned By Me'' item filters the list of projects to show projects which you actually own. The ''Trash'' item filters the list of projects to show projects which you own that are in the trash. Projects that are in the trash do not get deleted, they just aren't visible to other users.

== Creating and Uploading Projects ==

[[File:wp-project-action-buttons.png]]

To create a new empty project press the ''Create Project...'' button. To upload an existing ontology into a new project (either an OWL ontology or an OBO ontology) press the ''Upload Project ...'' button. In both cases a dialog will appear like the one shown below. Enter the name for the project (this need not be unique) and description of the project and press o.k.

[[File:wp-upload-dialog.png]]

=== Other tabs and portlets ===

WebProtégé has a configurable user interface, and each user can customize the layout and save it for future sessions. The user may choose from a list of existing tabs and add portlets dynamically from the user interface. It is also possible to create a new empty tab and add the needed portlets through drag-n-drop. More information on the layout configuration can be found [[WebProtegeLayoutConfig|here]].

== References ==

Further documentation and references on WebProtégé can be found [[WebProtege#References|here]].

'''Go back to [[WebProtege|WebProtégé main page]].'''

[[Category:WebProtege documentation]]

File:Wp-upload-dialog.png

2013-04-25T23:29:20Z

Matthewhorridge:

WebProtegeUsersGuide

2013-04-25T23:28:09Z

Matthewhorridge:

WebProtégé User Guide

'''WebProtégé''' is an open source, lightweight, web-based ontology editor.

__TOC__

'''Go back to [[WebProtege|WebProtégé main page]].'''

'''Looking for the user guide of the old WebProtege (release 1.0)? [[WebProtege1.0UsersGuide|Here]] it is.'''

= Home Screen =

When you open webprotege.stanford.edu in a browser you should see the list of public projects and various links to create an account or sign in (top right). You can download the ontologies in any publicly available project by clicking the download icon in the table. To open a project click on its name in the Project Name column.

[[File:wp-home-screen.png]]

To create and upload your own projects you need to have a user account and be signed in. If you don't have a user account you can create one using the "Sign Up for Account" button. To sign in click the "Sign In" link in the top right of the browser window. Enter your user name and password in the dialog that pops up. (You can also sign in with OpenId).

== Nav Bar ==

[[File:Wp-nav-bar.png]]

Once you are signed in you will see a side bar on the left hand side of the screen which offers different categories of projects to view. Clicking on any item in the side bar will filter the list of projects. The ''home'' item shows all projects which are owned by you and projects which you have read or write access to. The ''Owned By Me'' item filters the list of projects to show projects which you actually own. The ''Trash'' item filters the list of projects to show projects which you own that are in the trash. Projects that are in the trash do not get deleted, they just aren't visible to other users.

== Creating and Uploading Projects ==

[[File:wp-project-action-buttons.png]]

To create a new empty project press the ''Create Project...'' button. To upload an existing ontology into a new project (either an OWL ontology or an OBO ontology) press the ''Upload Project ...'' button. In both cases a dialog will appear. Enter the name for the project (this need not be unique) and description of the project and press o.k.

=== Other tabs and portlets ===

WebProtégé has a configurable user interface, and each user can customize the layout and save it for future sessions. The user may choose from a list of existing tabs and add portlets dynamically from the user interface. It is also possible to create a new empty tab and add the needed portlets through drag-n-drop. More information on the layout configuration can be found [[WebProtegeLayoutConfig|here]].

== References ==

Further documentation and references on WebProtégé can be found [[WebProtege#References|here]].

'''Go back to [[WebProtege|WebProtégé main page]].'''

[[Category:WebProtege documentation]]

WebProtegeUsersGuide

2013-04-25T23:26:33Z

Matthewhorridge:

WebProtégé User Guide

'''WebProtégé''' is an open source, lightweight, web-based ontology editor.

__TOC__

'''Go back to [[WebProtege|WebProtégé main page]].'''

'''Looking for the user guide of the old WebProtege (release 1.0)? [[WebProtege1.0UsersGuide|Here]] it is.'''

= Home Screen =

When you open webprotege.stanford.edu in a browser you should see the list of public projects and various links to create an account or sign in (top right). You can download the ontologies in any publicly available project by clicking the download icon in the table. To open a project click on its name in the Project Name column.

[[File:wp-home-screen.png]]

To create and upload your own projects you need to have a user account and be signed in. If you don't have a user account you can create one using the "Sign Up for Account" button. To sign in click the "Sign In" link in the top right of the browser window. Enter your user name and password in the dialog that pops up. (You can also sign in with OpenId).

== Nav Bar ==

[[File:Wp-nav-bar.png]]

Once you are signed in you will see a side bar on the left hand side of the screen which offers different categories of projects to view. Clicking on any item in the side bar will filter the list of projects. The ''home'' item shows all projects which are owned by you and projects which you have read or write access to. The ''Owned By Me'' item filters the list of projects to show projects which you actually own. The ''Trash'' item filters the list of projects to show projects which you own that are in the trash. Projects that are in the trash do not get deleted, they just aren't visible to other users.

== Creating and Uploading Projects ==

[[File:wp-project-action-buttons.png]]

=== Other tabs and portlets ===

WebProtégé has a configurable user interface, and each user can customize the layout and save it for future sessions. The user may choose from a list of existing tabs and add portlets dynamically from the user interface. It is also possible to create a new empty tab and add the needed portlets through drag-n-drop. More information on the layout configuration can be found [[WebProtegeLayoutConfig|here]].

== References ==

Further documentation and references on WebProtégé can be found [[WebProtege#References|here]].

'''Go back to [[WebProtege|WebProtégé main page]].'''

[[Category:WebProtege documentation]]

File:Wp-project-action-buttons.png

2013-04-25T23:25:55Z

Matthewhorridge:

WebProtegeUsersGuide

2013-04-25T23:23:57Z

Matthewhorridge:

WebProtégé User Guide

'''WebProtégé''' is an open source, lightweight, web-based ontology editor.

__TOC__

'''Go back to [[WebProtege|WebProtégé main page]].'''

'''Looking for the user guide of the old WebProtege (release 1.0)? [[WebProtege1.0UsersGuide|Here]] it is.'''

= Home Screen =

When you open webprotege.stanford.edu in a browser you should see the list of public projects and various links to create an account or sign in (top right). You can download the ontologies in any publicly available project by clicking the download icon in the table. To open a project click on its name in the Project Name column.

[[File:wp-home-screen.png]]

To create and upload your own projects you need to have a user account and be signed in. If you don't have a user account you can create one using the "Sign Up for Account" button. To sign in click the "Sign In" link in the top right of the browser window. Enter your user name and password in the dialog that pops up. (You can also sign in with OpenId).

== Nav Bar ==

[[File:Wp-nav-bar.png]]

Once you are signed in you will see a side bar on the left hand side of the screen which offers different categories of projects to view. Clicking on any item in the side bar will filter the list of projects. The ''home'' item shows all projects which are owned by you and projects which you have read or write access to. The ''Owned By Me'' item filters the list of projects to show projects which you actually own. The ''Trash'' item filters the list of projects to show projects which you own that are in the trash. Projects that are in the trash do not get deleted, they just aren't visible to other users.

=== Other tabs and portlets ===

WebProtégé has a configurable user interface, and each user can customize the layout and save it for future sessions. The user may choose from a list of existing tabs and add portlets dynamically from the user interface. It is also possible to create a new empty tab and add the needed portlets through drag-n-drop. More information on the layout configuration can be found [[WebProtegeLayoutConfig|here]].

== References ==

Further documentation and references on WebProtégé can be found [[WebProtege#References|here]].

'''Go back to [[WebProtege|WebProtégé main page]].'''

[[Category:WebProtege documentation]]

File:Wp-nav-bar.png

2013-04-25T23:23:13Z

Matthewhorridge: Matthewhorridge uploaded a new version of "File:Wp-nav-bar.png"

WebProtegeUsersGuide

2013-04-25T23:22:36Z

Matthewhorridge:

WebProtégé User Guide

'''WebProtégé''' is an open source, lightweight, web-based ontology editor.

__TOC__

'''Go back to [[WebProtege|WebProtégé main page]].'''

'''Looking for the user guide of the old WebProtege (release 1.0)? [[WebProtege1.0UsersGuide|Here]] it is.'''

= Home Screen =

When you open webprotege.stanford.edu in a browser you should see the list of public projects and various links to create an account or sign in (top right). You can download the ontologies in any publicly available project by clicking the download icon in the table. To open a project click on its name in the Project Name column.

[[File:wp-home-screen.png]]

To create and upload your own projects you need to have a user account and be signed in. If you don't have a user account you can create one using the "Sign Up for Account" button. To sign in click the "Sign In" link in the top right of the browser window. Enter your user name and password in the dialog that pops up. (You can also sign in with OpenId).

[[File:Wp-nav-bar.png]]

Once you are signed in you will see a side bar on the left hand side of the screen which offers different categories of projects to view. Clicking on any item in the side bar will filter the list of projects. The ''home'' item shows all projects which are owned by you and projects which you have read or write access to. The ''Owned By Me'' item filters the list of projects to show projects which you actually own. The ''Trash'' item filters the list of projects to show projects which you own that are in the trash. Projects that are in the trash do not get deleted, they just aren't visible to other users.

=== Other tabs and portlets ===

WebProtégé has a configurable user interface, and each user can customize the layout and save it for future sessions. The user may choose from a list of existing tabs and add portlets dynamically from the user interface. It is also possible to create a new empty tab and add the needed portlets through drag-n-drop. More information on the layout configuration can be found [[WebProtegeLayoutConfig|here]].

== References ==

Further documentation and references on WebProtégé can be found [[WebProtege#References|here]].

'''Go back to [[WebProtege|WebProtégé main page]].'''

[[Category:WebProtege documentation]]

WebProtegeUsersGuide

2013-04-25T23:21:47Z

Matthewhorridge:

WebProtégé User Guide

'''WebProtégé''' is an open source, lightweight, web-based ontology editor.

__TOC__

'''Go back to [[WebProtege|WebProtégé main page]].'''

'''Looking for the user guide of the old WebProtege (release 1.0)? [[WebProtege1.0UsersGuide|Here]] it is.'''

= Home Screen =

When you open webprotege.stanford.edu in a browser you should see the list of public projects and various links to create an account or sign in (top right). You can download the ontologies in any publicly available project by clicking the download icon in the table. To open a project click on its name in the Project Name column.

[[File:wp-home-screen.png]]

To create and upload your own projects you need to have a user account and be signed in. If you don't have a user account you can create one using the "Sign Up for Account" button. To sign in click the "Sign In" link in the top right of the browser window. Enter your user name and password in the dialog that pops up. (You can also sign in with OpenId).

Once you are signed in you will see a side bar on the left hand side of the screen which offers different categories of projects to view. Clicking on any item in the side bar will filter the list of projects. The ''home'' item shows all projects which are owned by you and projects which you have read or write access to. The ''Owned By Me'' item filters the list of projects to show projects which you actually own. The ''Trash'' item filters the list of projects to show projects which you own that are in the trash. Projects that are in the trash do not get deleted, they just aren't visible to other users.

[[File:Wp-nav-bar.png]]

=== Other tabs and portlets ===

WebProtégé has a configurable user interface, and each user can customize the layout and save it for future sessions. The user may choose from a list of existing tabs and add portlets dynamically from the user interface. It is also possible to create a new empty tab and add the needed portlets through drag-n-drop. More information on the layout configuration can be found [[WebProtegeLayoutConfig|here]].

== References ==

Further documentation and references on WebProtégé can be found [[WebProtege#References|here]].

'''Go back to [[WebProtege|WebProtégé main page]].'''

[[Category:WebProtege documentation]]

File:Wp-nav-bar.png

2013-04-25T23:18:48Z

Matthewhorridge:

WebProtegeUsersGuide

2013-04-25T23:18:36Z

Matthewhorridge:

WebProtégé User Guide

'''WebProtégé''' is an open source, lightweight, web-based ontology editor.

__TOC__

'''Go back to [[WebProtege|WebProtégé main page]].'''

'''Looking for the user guide of the old WebProtege (release 1.0)? [[WebProtege1.0UsersGuide|Here]] it is.'''

= Home Screen =

When you open webprotege.stanford.edu in a browser you should see the list of public projects and various links to create an account or sign in (top right). You can download the ontologies in any publicly available project by clicking the download icon in the table. To open a project click on its name in the Project Name column.

[[File:wp-home-screen.png]]

To create and upload your own projects you need to have a user account and be signed in. If you don't have a user account you can create one using the "Sign Up for Account" button. To sign in click the "Sign In" link in the top right of the browser window. Enter your user name and password in the dialog that pops up. (You can also sign in with OpenId).

=== Other tabs and portlets ===

WebProtégé has a configurable user interface, and each user can customize the layout and save it for future sessions. The user may choose from a list of existing tabs and add portlets dynamically from the user interface. It is also possible to create a new empty tab and add the needed portlets through drag-n-drop. More information on the layout configuration can be found [[WebProtegeLayoutConfig|here]].

== References ==

Further documentation and references on WebProtégé can be found [[WebProtege#References|here]].

'''Go back to [[WebProtege|WebProtégé main page]].'''

[[Category:WebProtege documentation]]

WebProtegeUsersGuide

2013-04-25T23:04:51Z

Matthewhorridge:

WebProtégé User Guide

'''WebProtégé''' is an open source, lightweight, web-based ontology editor.

__TOC__

'''Go back to [[WebProtege|WebProtégé main page]].'''

'''Looking for the user guide of the old WebProtege (release 1.0)? [[WebProtege1.0UsersGuide|Here]] it is.'''

= Home Screen =

When you open webprotege.stanford.edu in a browser you should see the list of public projects and various links to create an account or sign in (top right). You can download the ontologies in any publicly available project by clicking the download icon in the table. To open a project click on its name in the Project Name column.

[[File:wp-home-screen.png]]

=== Other tabs and portlets ===

WebProtégé has a configurable user interface, and each user can customize the layout and save it for future sessions. The user may choose from a list of existing tabs and add portlets dynamically from the user interface. It is also possible to create a new empty tab and add the needed portlets through drag-n-drop. More information on the layout configuration can be found [[WebProtegeLayoutConfig|here]].

== References ==

Further documentation and references on WebProtégé can be found [[WebProtege#References|here]].

'''Go back to [[WebProtege|WebProtégé main page]].'''

[[Category:WebProtege documentation]]

WebProtegeUsersGuide

2013-04-25T23:04:42Z

Matthewhorridge:

WebProtégé User Guide

'''WebProtégé''' is an open source, lightweight, web-based ontology editor.

__TOC__

'''Go back to [[WebProtege|WebProtégé main page]].'''

'''Looking for the user guide of the old WebProtege (release 1.0)? [[WebProtege1.0UsersGuide|Here]] it is.'''

= Home Screen =

When you open webprotege.stanford.edu in a browser you should see the list of public projects and various links to create an account or sign in (top right). You can download the ontologies in any publicly available project by clicking the download icon in the table. To open a project click on its name in the Project Name column.

[[File:wp-home-screen]]

=== Other tabs and portlets ===

WebProtégé has a configurable user interface, and each user can customize the layout and save it for future sessions. The user may choose from a list of existing tabs and add portlets dynamically from the user interface. It is also possible to create a new empty tab and add the needed portlets through drag-n-drop. More information on the layout configuration can be found [[WebProtegeLayoutConfig|here]].

== References ==

Further documentation and references on WebProtégé can be found [[WebProtege#References|here]].

'''Go back to [[WebProtege|WebProtégé main page]].'''

[[Category:WebProtege documentation]]

File:Wp-home-screen.png

2013-04-25T23:00:16Z

Matthewhorridge:

WebProtegeUsersGuide

2013-04-25T22:59:37Z

Matthewhorridge: (checkpoint save)

WebProtégé User Guide

'''WebProtégé''' is an open source, lightweight, web-based ontology editor.

__TOC__

'''Go back to [[WebProtege|WebProtégé main page]].'''

'''Looking for the user guide of the old WebProtege (release 1.0)? [[WebProtege1.0UsersGuide|Here]] it is.'''

= Home Screen =

When you open webprotege.stanford.edu in a browser you should see the list of public projects and various links to create an account or sign in (top right).

[[File:wp-home-screen]]

=== Other tabs and portlets ===

WebProtégé has a configurable user interface, and each user can customize the layout and save it for future sessions. The user may choose from a list of existing tabs and add portlets dynamically from the user interface. It is also possible to create a new empty tab and add the needed portlets through drag-n-drop. More information on the layout configuration can be found [[WebProtegeLayoutConfig|here]].

== References ==

Further documentation and references on WebProtégé can be found [[WebProtege#References|here]].

'''Go back to [[WebProtege|WebProtégé main page]].'''

[[Category:WebProtege documentation]]