https://protegewiki.stanford.edu/api.php?action=feedcontributions&user=Samsontu&feedformat=atomProtege Wiki - User contributions [en]2024-03-29T02:05:12ZUser contributionsMediaWiki 1.27.7https://protegewiki.stanford.edu/index.php?title=Main_Page&diff=13816Main Page2022-02-18T06:55:35Z<p>Samsontu: </p>
<hr />
<div>__NOTOC__<br />
= <span style="color:#2c3e50;"> Welcome to the Prot&eacute;g&eacute; wiki! </span> =<br />
<br />
[[File:WP-classes.png|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[WebProtege|WebProt&eacute;g&eacute;]] - a powerful collaborative ontology development environment for the Web </span>]]<br />
<br />
[[File:Protege5.5.jpg|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[Protege4UserDocs|Prot&eacute;g&eacute; Desktop]] - a fully-fledged OWL 2 ontology editor for the desktops</span>]]<br />
<br />
[https://protege.stanford.edu Prot&eacute;g&eacute;] 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. <br />
<br />
''' Quick links: [https://webprotege.stanford.edu WebProt&eacute;g&eacute; server], Prot&eacute;g&eacute; Desktop [https://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], [https://protege.stanford.edu Prot&eacute;g&eacute; website] '''<br />
<br />
= <span style="color:#2c3e50;"> User Documentation </span>=<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
* [[WebProtege|Overview]]<br />
* [[WebProtegeUsersGuide|User's Guide]]<br />
* [https://github.com/protegeproject/webprotege/wiki/WebProtégé-4.0.0-beta-x-Installation Administrator's Guide] - download and installation instructions<br />
* Use WebProt&eacute;g&eacute; now on our Stanford-hosted server: http://webprotege.stanford.edu<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [http://protegeproject.github.io/protege/ Prot&eacute;g&eacute; Desktop documentation] ([https://github.com/protegeproject/protege-distribution/releases release notes], [http://protegeproject.github.io/protege/installation/ installation instructions], [http://protege.stanford.edu/products.php#desktop-protege Protege Desktop download], [[Protege_Desktop_Old_Versions|older Protege releases download]])<br />
* [[Protege3UserDocs|Older Prot&eacute;g&eacute; releases documentation (version 3.x)]]<br />
* [[Protege-OWL_4_FAQ|Frequently Asked Questions (FAQ)]]<br />
<br />
=== <span style="color:#2c3e50;"> Tutorials and Getting Started</span> ===<br />
* [http://protegeproject.github.io/protege/getting-started/ Getting started with the Protege Desktop editor] <br />
Prot&eacute;g&eacute; Tutorials<br />
* [https://www.michaeldebellis.com/post/new-protege-pizza-tutorial Michael DeBellis's updated Prot&eacute;g&eacute; Pizza Tutorial]<br />
* [http://owl.cs.manchester.ac.uk/publications/talks-and-tutorials/protg-owl-tutorial/ The original Prot&eacute;g&eacute; OWL Tutorial: A step-by-step guide to modeling in OWL using the Prot&eacute;g&eacute; OWL tools]<br />
<br />
Background Information<br />
* [http://protege.stanford.edu/publications/ontology_development/ontology101.html Ontology Development 101: A Guide to creating your first ontology]<br />
* [http://www.cs.man.ac.uk/~stevensr/menupages/background.php Brief introduction to ontologies], by Robert Stevens<br />
* Semantic Web Best Practices and Deployment Working Group's [http://www.w3.org/2001/sw/BestPractices/Tutorials Semantic Web Tutorials] page<br />
* [http://arxiv.org/abs/1201.4089 A Description Logic Primer]<br />
<br />
Older documentation, illustrated with Prot&eacute;g&eacute; 4 user interface, but substantially correct.<br />
* [[Pr4_UG | Protege Desktop User's Guide]] - a guide on how to use Protege to create, edit, and inspect ontologies<br />
* [[Protege4Pizzas10Minutes | Pizzas in 10 minutes: A demo of modeling shortcuts]] - a quickstart guide to creating your first OWL ontology<br />
<br />
= <span style="color:#2c3e50;"> Developer Documentation </span> =<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
<br />
Please see the [https://github.com/protegeproject/webprotege WebProt&eacute;g&eacute; GitHub page]<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [[Protege5DevDocs|Prot&eacute;g&eacute; Desktop 5.x developer documentation]]<br />
<br />
* [[ProtegeQAGuide|Guide to Quality Assurance]]<br />
<br />
<br />
= <span style="color:#2c3e50;"> Download and Support </span> =<br />
<br />
To download Prot&eacute;g&eacute; or WebProt&eacute;g&eacute; please visit our [http://protege.stanford.edu homepage]. To use the WebProt&eacute;g&eacute; server hosted at Stanford, please go to: http://webprotege.stanford.edu. <br />
<br />
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].<br />
<br />
Follow our [http://www.youtube.com/user/TheProtegeProject YouTube channel] featuring screencasts showing different features of Prot&eacute;g&eacute; and WebProt&eacute;g&eacute;.<br />
<br />
<br />
= <span style="color:#2c3e50;"> Wiki Help </span> =<br />
If you are new to using a Wiki, please see the [[Help:Contents|Help page]] page for links to User's Guides, etc. <br />
<br />
The [[Help:Contents|Help page]] also has suggestions for where to find help with using the Prot&eacute;g&eacute; application.</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Main_Page&diff=13815Main Page2022-02-18T06:53:58Z<p>Samsontu: </p>
<hr />
<div>__NOTOC__<br />
= <span style="color:#2c3e50;"> Welcome to the Prot&eacute;g&eacute; wiki! </span> =<br />
<br />
[[File:WP-classes.png|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[WebProtege|WebProt&eacute;g&eacute;]] - a powerful collaborative ontology development environment for the Web </span>]]<br />
<br />
[[File:Protege5.5.jpg|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[Protege4UserDocs|Prot&eacute;g&eacute; Desktop]] - a fully-fledged OWL 2 ontology editor for the desktops</span>]]<br />
<br />
[https://protege.stanford.edu Prot&eacute;g&eacute;] 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. <br />
<br />
''' Quick links: [https://webprotege.stanford.edu WebProt&eacute;g&eacute; server], Prot&eacute;g&eacute; Desktop [https://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], [https://protege.stanford.edu Prot&eacute;g&eacute; website] '''<br />
<br />
= <span style="color:#2c3e50;"> User Documentation </span>=<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
* [[WebProtege|Overview]]<br />
* [[WebProtegeUsersGuide|User's Guide]]<br />
* [https://github.com/protegeproject/webprotege/wiki/WebProtégé-4.0.0-beta-x-Installation Administrator's Guide] - download and installation instructions<br />
* Use WebProt&eacute;g&eacute; now on our Stanford-hosted server: http://webprotege.stanford.edu<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [http://protegeproject.github.io/protege/ Prot&eacute;g&eacute; Desktop documentation] ([https://github.com/protegeproject/protege-distribution/releases release notes], [http://protegeproject.github.io/protege/installation/ installation instructions], [http://protege.stanford.edu/products.php#desktop-protege Protege Desktop download], [[Protege_Desktop_Old_Versions|older Protege releases download]])<br />
* [[Protege3UserDocs|Older Prot&eacute;g&eacute; releases documentation (version 3.x)]]<br />
* [[Protege-OWL_4_FAQ|Frequently Asked Questions (FAQ)]]<br />
<br />
=== <span style="color:#2c3e50;"> Tutorials and Getting Started</span> ===<br />
* [http://protegeproject.github.io/protege/getting-started/ Getting started with the Protege Desktop editor] <br />
Prot&eacute;g&eacute; Tutorials<br />
* [https://www.michaeldebellis.com/post/new-protege-pizza-tutorial Michael DeBellis's updated Prot&eacute;g&eacute; Pizza Tutorial]<br />
* [http://owl.cs.manchester.ac.uk/publications/talks-and-tutorials/protg-owl-tutorial/ The original Prot&eacute;g&eacute; OWL Tutorial: A step-by-step guide to modeling in OWL using the Prot&eacute;g&eacute; OWL tools]<br />
<br />
Background Information<br />
* [http://protege.stanford.edu/publications/ontology_development/ontology101.html Ontology Development 101: A Guide to creating your first ontology]<br />
* [http://www.cs.man.ac.uk/~stevensr/menupages/background.php Brief introduction to ontologies], by Robert Stevens<br />
* Semantic Web Best Practices and Deployment Working Group's [http://www.w3.org/2001/sw/BestPractices/Tutorials Semantic Web Tutorials] page<br />
* [http://arxiv.org/abs/1201.4089 A Description Logic Primer]<br />
<br />
Older documentation, illustrated with Prot&eacute;g&eacute; 4 user interface, but substantially correct.<br />
* [[Pr4_UG | Protege Desktop User's Guide]] - a guide on how to use Protege to create, edit, and inspect ontologies<br />
* [[Protege4Pizzas10Minutes | Pizzas in 10 minutes: A demo of modeling shortcuts]] - a quickstart guide to creating your first OWL ontology<br />
<br />
= <span style="color:#2c3e50;"> Developer Documentation </span> =<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
<br />
Please see the [https://github.com/protegeproject/webprotege WebProt&eacute;g&eacute; GitHub page]<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [[Protege5DevDocs|Prot&eacute;g&eacute; Desktop 5.x]]<br />
<br />
* [[ProtegeQAGuide|Guide to Quality Assurance]]<br />
<br />
<br />
= <span style="color:#2c3e50;"> Download and Support </span> =<br />
<br />
To download Prot&eacute;g&eacute; or WebProt&eacute;g&eacute; please visit our [http://protege.stanford.edu homepage]. To use the WebProt&eacute;g&eacute; server hosted at Stanford, please go to: http://webprotege.stanford.edu. <br />
<br />
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].<br />
<br />
Follow our [http://www.youtube.com/user/TheProtegeProject YouTube channel] featuring screencasts showing different features of Prot&eacute;g&eacute; and WebProt&eacute;g&eacute;.<br />
<br />
<br />
= <span style="color:#2c3e50;"> Wiki Help </span> =<br />
If you are new to using a Wiki, please see the [[Help:Contents|Help page]] page for links to User's Guides, etc. <br />
<br />
The [[Help:Contents|Help page]] also has suggestions for where to find help with using the Prot&eacute;g&eacute; application.</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Main_Page&diff=13814Main Page2022-02-18T06:53:38Z<p>Samsontu: </p>
<hr />
<div>__NOTOC__<br />
= <span style="color:#2c3e50;"> Welcome to the Prot&eacute;g&eacute; wiki! </span> =<br />
<br />
[[File:WP-classes.png|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[WebProtege|WebProt&eacute;g&eacute;]] - a powerful collaborative ontology development environment for the Web </span>]]<br />
<br />
[[File:Protege5.5.jpg|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[Protege4UserDocs|Prot&eacute;g&eacute; Desktop]] - a fully-fledged OWL 2 ontology editor for the desktops</span>]]<br />
<br />
[https://protege.stanford.edu Prot&eacute;g&eacute;] 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. <br />
<br />
''' Quick links: [https://webprotege.stanford.edu WebProt&eacute;g&eacute; server], Prot&eacute;g&eacute; Desktop [https://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], [https://protege.stanford.edu Prot&eacute;g&eacute; website] '''<br />
<br />
= <span style="color:#2c3e50;"> User Documentation </span>=<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
* [[WebProtege|Overview]]<br />
* [[WebProtegeUsersGuide|User's Guide]]<br />
* [https://github.com/protegeproject/webprotege/wiki/WebProtégé-4.0.0-beta-x-Installation Administrator's Guide] - download and installation instructions<br />
* Use WebProt&eacute;g&eacute; now on our Stanford-hosted server: http://webprotege.stanford.edu<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [http://protegeproject.github.io/protege/ Prot&eacute;g&eacute; Desktop documentation] ([https://github.com/protegeproject/protege-distribution/releases release notes], [http://protegeproject.github.io/protege/installation/ installation instructions], [http://protege.stanford.edu/products.php#desktop-protege Protege Desktop download], [[Protege_Desktop_Old_Versions|older Protege releases download]])<br />
* [[Protege3UserDocs|Older Prot&eacute;g&eacute; releases documentation (version 3.x)]]<br />
* [[Protege-OWL_4_FAQ|Frequently Asked Questions (FAQ)]]<br />
<br />
=== <span style="color:#2c3e50;"> Tutorials and Getting Started</span> ===<br />
* [http://protegeproject.github.io/protege/getting-started/ Getting started with the Protege Desktop editor] <br />
rot&eacute;g&eacute; Tutorials<br />
* [https://www.michaeldebellis.com/post/new-protege-pizza-tutorial Michael DeBellis's updated Prot&eacute;g&eacute; Pizza Tutorial]<br />
* [http://owl.cs.manchester.ac.uk/publications/talks-and-tutorials/protg-owl-tutorial/ The original Prot&eacute;g&eacute; OWL Tutorial: A step-by-step guide to modeling in OWL using the Prot&eacute;g&eacute; OWL tools]<br />
<br />
Background Information<br />
* [http://protege.stanford.edu/publications/ontology_development/ontology101.html Ontology Development 101: A Guide to creating your first ontology]<br />
* [http://www.cs.man.ac.uk/~stevensr/menupages/background.php Brief introduction to ontologies], by Robert Stevens<br />
* Semantic Web Best Practices and Deployment Working Group's [http://www.w3.org/2001/sw/BestPractices/Tutorials Semantic Web Tutorials] page<br />
* [http://arxiv.org/abs/1201.4089 A Description Logic Primer]<br />
<br />
Older documentation, illustrated with Prot&eacute;g&eacute; 4 user interface, but substantially correct.<br />
* [[Pr4_UG | Protege Desktop User's Guide]] - a guide on how to use Protege to create, edit, and inspect ontologies<br />
* [[Protege4Pizzas10Minutes | Pizzas in 10 minutes: A demo of modeling shortcuts]] - a quickstart guide to creating your first OWL ontology<br />
<br />
= <span style="color:#2c3e50;"> Developer Documentation </span> =<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
<br />
Please see the [https://github.com/protegeproject/webprotege WebProt&eacute;g&eacute; GitHub page]<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [[Protege5DevDocs|Prot&eacute;g&eacute; Desktop 5.x]]<br />
<br />
* [[ProtegeQAGuide|Guide to Quality Assurance]]<br />
<br />
<br />
= <span style="color:#2c3e50;"> Download and Support </span> =<br />
<br />
To download Prot&eacute;g&eacute; or WebProt&eacute;g&eacute; please visit our [http://protege.stanford.edu homepage]. To use the WebProt&eacute;g&eacute; server hosted at Stanford, please go to: http://webprotege.stanford.edu. <br />
<br />
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].<br />
<br />
Follow our [http://www.youtube.com/user/TheProtegeProject YouTube channel] featuring screencasts showing different features of Prot&eacute;g&eacute; and WebProt&eacute;g&eacute;.<br />
<br />
<br />
= <span style="color:#2c3e50;"> Wiki Help </span> =<br />
If you are new to using a Wiki, please see the [[Help:Contents|Help page]] page for links to User's Guides, etc. <br />
<br />
The [[Help:Contents|Help page]] also has suggestions for where to find help with using the Prot&eacute;g&eacute; application.</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Main_Page&diff=13813Main Page2022-02-18T06:49:58Z<p>Samsontu: </p>
<hr />
<div>__NOTOC__<br />
= <span style="color:#2c3e50;"> Welcome to the Prot&eacute;g&eacute; wiki! </span> =<br />
<br />
[[File:WP-classes.png|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[WebProtege|WebProt&eacute;g&eacute;]] - a powerful collaborative ontology development environment for the Web </span>]]<br />
<br />
[[File:Protege5.5.jpg|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[Protege4UserDocs|Prot&eacute;g&eacute; Desktop]] - a fully-fledged OWL 2 ontology editor for the desktops</span>]]<br />
<br />
[https://protege.stanford.edu Prot&eacute;g&eacute;] 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. <br />
<br />
''' Quick links: [https://webprotege.stanford.edu WebProt&eacute;g&eacute; server], Prot&eacute;g&eacute; Desktop [https://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], [https://protege.stanford.edu Prot&eacute;g&eacute; website] '''<br />
<br />
= <span style="color:#2c3e50;"> User Documentation </span>=<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
* [[WebProtege|Overview]]<br />
* [[WebProtegeUsersGuide|User's Guide]]<br />
* [https://github.com/protegeproject/webprotege/wiki/WebProtégé-4.0.0-beta-x-Installation Administrator's Guide] - download and installation instructions<br />
* Use WebProt&eacute;g&eacute; now on our Stanford-hosted server: http://webprotege.stanford.edu<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [http://protegeproject.github.io/protege/ Prot&eacute;g&eacute; Desktop documentation] ([https://github.com/protegeproject/protege-distribution/releases release notes], [http://protegeproject.github.io/protege/installation/ installation instructions], [http://protege.stanford.edu/products.php#desktop-protege Protege Desktop download], [[Protege_Desktop_Old_Versions|older Protege releases download]])<br />
* [[Protege3UserDocs|Older Prot&eacute;g&eacute; releases documentation (version 3.x)]]<br />
* [[Protege-OWL_4_FAQ|Frequently Asked Questions (FAQ)]]<br />
<br />
=== <span style="color:#2c3e50;"> Tutorials and Getting Started</span> ===<br />
* [http://protegeproject.github.io/protege/getting-started/ Getting started with the Protege Desktop editor] <br />
Tutorials<br />
* [https://www.michaeldebellis.com/post/new-protege-pizza-tutorial Michael DeBellis's updated Prot&eacute;g&eacute; Pizza Tutorial]<br />
* [http://owl.cs.manchester.ac.uk/publications/talks-and-tutorials/protg-owl-tutorial/ The original Prot&eacute;g&eacute; OWL Tutorial: A step-by-step guide to modeling in OWL using the Prot&eacute;g&eacute; OWL tools]<br />
<br />
Background Information<br />
* [http://protege.stanford.edu/publications/ontology_development/ontology101.html Ontology Development 101: A Guide to creating your first ontology]<br />
* [http://www.cs.man.ac.uk/~stevensr/menupages/background.php Brief introduction to ontologies], by Robert Stevens<br />
* Semantic Web Best Practices and Deployment Working Group's [http://www.w3.org/2001/sw/BestPractices/Tutorials Semantic Web Tutorials] page<br />
* [http://arxiv.org/abs/1201.4089 A Description Logic Primer]<br />
<br />
Older documentation, illustrated with Prot&eacute;g&eacute; 4 user interface, but substantially correct.<br />
* [[Pr4_UG | Protege Desktop User's Guide]] - a guide on how to use Protege to create, edit, and inspect ontologies<br />
* [[Protege4Pizzas10Minutes | Pizzas in 10 minutes: A demo of modeling shortcuts]] - a quickstart guide to creating your first OWL ontology<br />
<br />
= <span style="color:#2c3e50;"> Developer Documentation </span> =<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
<br />
Please see the [https://github.com/protegeproject/webprotege WebProt&eacute;g&eacute; GitHub page]<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [[Protege5DevDocs|Prot&eacute;g&eacute; Desktop 5.x]]<br />
<br />
* [[ProtegeQAGuide|Guide to Quality Assurance]]<br />
<br />
<br />
= <span style="color:#2c3e50;"> Download and Support </span> =<br />
<br />
To download Prot&eacute;g&eacute; or WebProt&eacute;g&eacute; please visit our [http://protege.stanford.edu homepage]. To use the WebProt&eacute;g&eacute; server hosted at Stanford, please go to: http://webprotege.stanford.edu. <br />
<br />
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].<br />
<br />
Follow our [http://www.youtube.com/user/TheProtegeProject YouTube channel] featuring screencasts showing different features of Prot&eacute;g&eacute; and WebProt&eacute;g&eacute;.<br />
<br />
<br />
= <span style="color:#2c3e50;"> Wiki Help </span> =<br />
If you are new to using a Wiki, please see the [[Help:Contents|Help page]] page for links to User's Guides, etc. <br />
<br />
The [[Help:Contents|Help page]] also has suggestions for where to find help with using the Prot&eacute;g&eacute; application.</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Main_Page&diff=13812Main Page2022-02-18T06:15:27Z<p>Samsontu: </p>
<hr />
<div>__NOTOC__<br />
= <span style="color:#2c3e50;"> Welcome to the Prot&eacute;g&eacute; wiki! </span> =<br />
<br />
[[File:WP-classes.png|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[WebProtege|WebProt&eacute;g&eacute;]] - a powerful collaborative ontology development environment for the Web </span>]]<br />
<br />
[[File:Protege5.5.jpg|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[Protege4UserDocs|Prot&eacute;g&eacute; Desktop]] - a fully-fledged OWL 2 ontology editor for the desktops</span>]]<br />
<br />
[https://protege.stanford.edu Prot&eacute;g&eacute;] 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. <br />
<br />
''' Quick links: [https://webprotege.stanford.edu WebProt&eacute;g&eacute; server], Prot&eacute;g&eacute; Desktop [https://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], [https://protege.stanford.edu Prot&eacute;g&eacute; website] '''<br />
<br />
= <span style="color:#2c3e50;"> User Documentation </span>=<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
* [[WebProtege|Overview]]<br />
* [[WebProtegeUsersGuide|User's Guide]]<br />
* [https://github.com/protegeproject/webprotege/wiki/WebProtégé-4.0.0-beta-x-Installation Administrator's Guide] - download and installation instructions<br />
* Use WebProt&eacute;g&eacute; now on our Stanford-hosted server: http://webprotege.stanford.edu<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [http://protegeproject.github.io/protege/ Prot&eacute;g&eacute; Desktop documentation] ([https://github.com/protegeproject/protege-distribution/releases release notes], [http://protegeproject.github.io/protege/installation/ installation instructions], [http://protege.stanford.edu/products.php#desktop-protege Protege Desktop download], [[Protege_Desktop_Old_Versions|older Protege releases download]])<br />
* [http://protegeproject.github.io/protege/views/ Views], [http://protegeproject.github.io/protege/menus/ Menus], [http://protegeproject.github.io/protege/class-expression-syntax/ Class Expression Syntax] - a short guide to some of the desktop Prot&eacute;g&eacute; interface components<br />
* [[Protege3UserDocs|Older Prot&eacute;g&eacute; releases documentation (version 3.x)]]<br />
* [[Protege-OWL_4_FAQ|Frequently Asked Questions (FAQ)]]<br />
<br />
=== <span style="color:#2c3e50;"> Tutorials and Getting Started</span> ===<br />
* [http://protegeproject.github.io/protege/getting-started/ Getting started with the Protege Desktop editor] <br />
Tutorials<br />
* [https://www.michaeldebellis.com/post/new-protege-pizza-tutorial Michael DeBellis's updated Prot&eacute;g&eacute; Pizza Tutorial]<br />
* [http://owl.cs.manchester.ac.uk/publications/talks-and-tutorials/protg-owl-tutorial/ The original Prot&eacute;g&eacute; OWL Tutorial: A step-by-step guide to modeling in OWL using the Prot&eacute;g&eacute; OWL tools]<br />
<br />
Background Information<br />
* [http://protege.stanford.edu/publications/ontology_development/ontology101.html Ontology Development 101: A Guide to creating your first ontology]<br />
* [http://www.cs.man.ac.uk/~stevensr/menupages/background.php Brief introduction to ontologies], by Robert Stevens<br />
* Semantic Web Best Practices and Deployment Working Group's [http://www.w3.org/2001/sw/BestPractices/Tutorials Semantic Web Tutorials] page<br />
* [http://arxiv.org/abs/1201.4089 A Description Logic Primer]<br />
<br />
Older documentation, illustrated with Prot&eacute;g&eacute; 4 user interface, but substantially correct.<br />
* [[Pr4_UG | Protege Desktop User's Guide]] - a guide on how to use Protege to create, edit, and inspect ontologies<br />
* [[Protege4Pizzas10Minutes | Pizzas in 10 minutes: A demo of modeling shortcuts]] - a quickstart guide to creating your first OWL ontology<br />
<br />
= <span style="color:#2c3e50;"> Developer Documentation </span> =<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
<br />
Please see the [https://github.com/protegeproject/webprotege WebProt&eacute;g&eacute; GitHub page]<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [[Protege5DevDocs|Prot&eacute;g&eacute; Desktop 5.x]]<br />
<br />
* [[ProtegeQAGuide|Guide to Quality Assurance]]<br />
<br />
<br />
= <span style="color:#2c3e50;"> Download and Support </span> =<br />
<br />
To download Prot&eacute;g&eacute; or WebProt&eacute;g&eacute; please visit our [http://protege.stanford.edu homepage]. To use the WebProt&eacute;g&eacute; server hosted at Stanford, please go to: http://webprotege.stanford.edu. <br />
<br />
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].<br />
<br />
Follow our [http://www.youtube.com/user/TheProtegeProject YouTube channel] featuring screencasts showing different features of Prot&eacute;g&eacute; and WebProt&eacute;g&eacute;.<br />
<br />
<br />
= <span style="color:#2c3e50;"> Wiki Help </span> =<br />
If you are new to using a Wiki, please see the [[Help:Contents|Help page]] page for links to User's Guides, etc. <br />
<br />
The [[Help:Contents|Help page]] also has suggestions for where to find help with using the Prot&eacute;g&eacute; application.</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Main_Page&diff=13811Main Page2022-02-18T05:37:51Z<p>Samsontu: </p>
<hr />
<div>__NOTOC__<br />
= <span style="color:#2c3e50;"> Welcome to the Prot&eacute;g&eacute; wiki! </span> =<br />
<br />
[[File:WP-classes.png|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[WebProtege|WebProt&eacute;g&eacute;]] - a powerful collaborative ontology development environment for the Web </span>]]<br />
<br />
[[File:Protege5.5.jpg|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[Protege4UserDocs|Prot&eacute;g&eacute; Desktop]] - a fully-fledged OWL 2 ontology editor for the desktops</span>]]<br />
<br />
[https://protege.stanford.edu Prot&eacute;g&eacute;] 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. <br />
<br />
''' Quick links: [https://webprotege.stanford.edu WebProt&eacute;g&eacute; server], Prot&eacute;g&eacute; Desktop [https://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], [https://protege.stanford.edu Prot&eacute;g&eacute; website] '''<br />
<br />
= <span style="color:#2c3e50;"> User Documentation </span>=<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
* [[WebProtege|Overview]]<br />
* [[WebProtegeUsersGuide|User's Guide]]<br />
* [https://github.com/protegeproject/webprotege/wiki/WebProtégé-4.0.0-beta-x-Installation Administrator's Guide] - download and installation instructions<br />
* Use WebProt&eacute;g&eacute; now on our Stanford-hosted server: http://webprotege.stanford.edu<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [http://protegeproject.github.io/protege/ Prot&eacute;g&eacute; Desktop documentation] ([https://github.com/protegeproject/protege-distribution/releases release notes], [http://protegeproject.github.io/protege/installation/ installation instructions], [http://protege.stanford.edu/products.php#desktop-protege Protege Desktop download], [[Protege_Desktop_Old_Versions|older Protege releases download]])<br />
* [http://protegeproject.github.io/protege/views/ Views], [http://protegeproject.github.io/protege/menus/ Menus], [http://protegeproject.github.io/protege/class-expression-syntax/ Class Expression Syntax] - a short guide to some of the desktop Prot&eacute;g&eacute; interface components<br />
* [[Protege3UserDocs|Older Prot&eacute;g&eacute; releases documentation (version 3.x)]]<br />
* [[Protege-OWL_4_FAQ|Frequently Asked Questions (FAQ)]]<br />
<br />
=== <span style="color:#2c3e50;"> Tutorials and Getting Started</span> ===<br />
* [http://protegeproject.github.io/protege/getting-started/ Getting started with the Protege Desktop editor] <br />
Tutorials<br />
* [https://www.michaeldebellis.com/post/new-protege-pizza-tutorial Michael DeBellis's updated Prot&eacute;g&eacute; Pizza Tutorial]<br />
* [http://owl.cs.manchester.ac.uk/publications/talks-and-tutorials/protg-owl-tutorial/ The original Prot&eacute;g&eacute; OWL Tutorial: A step-by-step guide to modeling in OWL using the Prot&eacute;g&eacute; OWL tools]<br />
<br />
Background Information<br />
* [http://protege.stanford.edu/publications/ontology_development/ontology101.html Ontology Development 101: A Guide to creating your first ontology]<br />
* [http://www.cs.man.ac.uk/~stevensr/menupages/background.php Brief introduction to ontologies], by Robert Stevens<br />
* Semantic Web Best Practices and Deployment Working Group's [http://www.w3.org/2001/sw/BestPractices/Tutorials Semantic Web Tutorials] page<br />
* [http://arxiv.org/abs/1201.4089 A Description Logic Primer]<br />
<br />
Older documentation, illustrated with Prot&eacute;g&eacute; 4 user interface, but substantially correct.<br />
* [[Pr4_UG | Protege Desktop User's Guide]] - a guide on how to use Protege to create, edit, and inspect ontologies<br />
* [[Protege4Pizzas10Minutes | Pizzas in 10 minutes: A demo of modeling shortcuts]] - a quickstart guide to creating your first OWL ontology<br />
<br />
= <span style="color:#2c3e50;"> Developer Documentation </span> =<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
<br />
Please see the [https://github.com/protegeproject/webprotege WebProt&eacute;g&eacute; GitHub page]<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [[Protege5DevDocs|Prot&eacute;g&eacute; Desktop 5.x]]<br />
* [[Protege4DevDocs|Prot&eacute;g&eacute; Desktop 4.x]]<br />
* [[Protege3DevDocs|Prot&eacute;g&eacute; Desktop 3.x]]<br />
<br />
* [[ProtegeQAGuide|Guide to Quality Assurance]]<br />
<br />
<br />
= <span style="color:#2c3e50;"> Download and Support </span> =<br />
<br />
To download Prot&eacute;g&eacute; or WebProt&eacute;g&eacute; please visit our [http://protege.stanford.edu homepage]. To use the WebProt&eacute;g&eacute; server hosted at Stanford, please go to: http://webprotege.stanford.edu. <br />
<br />
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].<br />
<br />
Follow our [http://www.youtube.com/user/TheProtegeProject YouTube channel] featuring screencasts showing different features of Prot&eacute;g&eacute; and WebProt&eacute;g&eacute;.<br />
<br />
<br />
= <span style="color:#2c3e50;"> Wiki Help </span> =<br />
If you are new to using a Wiki, please see the [[Help:Contents|Help page]] page for links to User's Guides, etc. <br />
<br />
The [[Help:Contents|Help page]] also has suggestions for where to find help with using the Prot&eacute;g&eacute; application.</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=File:Protege5.5.jpg&diff=13810File:Protege5.5.jpg2022-02-18T05:36:30Z<p>Samsontu: Protege 5.5 class hierarchy and editor</p>
<hr />
<div>Protege 5.5 class hierarchy and editor</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=ELK&diff=13808ELK2022-02-18T05:05:02Z<p>Samsontu: </p>
<hr />
<div>{{Plugin<br />
|Description=ELK is a free and open source reasoner for the lightweight ontology language OWL 2 EL.<br />
|PluginType=Reasoner<br />
|ForApplication1=Protege-OWL<br />
|HomepageURL=https://www.cs.ox.ac.uk/isg/tools/ELK/<br />
|DeveloperID1=Yevgeny Kazakov<br />
|DeveloperID2=Markus Krötzsch<br />
|DeveloperID3=František Simančík<br />
|DeveloperID4=Pavel Klinov<br />
|DeveloperID5=Peter Skocovsky<br />
|LastUpdated=January 11, 2016<br />
|Topic1=Reasoning<br />
|Topic2=Inference<br />
|License=Apache License 2.0<br />
|Affiliation1=University of Oxford<br />
|Affiliation2=University of Ulm<br />
}}<br />
<div style="clear: both; "></div><br />
The ELK reasoner is based on Java and can be controlled using the [http://owlapi.sourceforge.net/ OWL API], Protégé, the [[Snow Owl]] ontology editor, or a basic command line interface. ELK is available under the Apache License 2.0.<br />
<br />
ELK is very fast. It can classify the SNOMED CT ontology with around 300,000 classes in less than 4 seconds on a modern laptop (details can be found in a [http://korrekt.org/page/Concurrent_Classification_of_EL_Ontologies_(Technical_Report) technical report]). This is achieved by highly optimized consequence-based reasoning algorithms that can also take advantage of multi-core CPUs.<br />
<br />
ELK can be run in all operating systems that support Java 1.6 or above, but early releases do not yet support all features of OWL 2 EL. For further details, please see the [https://github.com/liveontologies/elk-reasoner/wiki online documentation]. The [http://groups.google.com/group/elk-reasoner-discussion ELK reasoner discussion group] is available for further discussions.</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Setting_Heap_Size&diff=13807Setting Heap Size2022-02-18T04:59:06Z<p>Samsontu: </p>
<hr />
<div><span style="font-weight:bold;font-size:18px;">Setting the Heap Size</span><br />
<br />
<br />
<span style="font-weight:bold;font-size:16px;">Recommendations for setting the heap size (read first!)</span><br />
<br />
<br />
You must be careful about setting the heap size parameter. If you set it too low then you will get "out of memory" errors. If you set it too high then your system will hang or you will suffer poor performance because parts of the jvm will be swapped in and out of memory. A rule of thumb is that you should not set this parameter larger than about 80% of your free physical memory. On Windows XP machines you can determine your free physical memory from the Performance tab of the Task Manager application. On Mac machines, click the apple (upper left hand corner and "about this mac"). On Linux machines, you can use the wonderful proc filesystem and look at the meminfo "file".<br />
<br />
Boosting the heap size parameter will allow you to read in larger file-based projects. It will also improve the performance of the database back-end since more memory is available for caching.<br />
<br />
The most common source of very slow performance on older systems (or laptops) is having the heap size set too large. If your system does not have 100MB of free memory then even the Protege default value is too big and you should make it smaller (or buy more memory). <br />
<br />
The best way to know if you have succeeded in changing the memory settings is to look at the console when Protege starts up. Protege will print out the memory settings as they start. The console or the log during startup will look something like this:<br />
<pre><br />
INFO 11:34:25 ------------------------------------ Protege -----------------------------------<br />
INFO 11:34:25 Protege Desktop<br />
INFO 11:34:25 Version 5.5.0, Build <br />
INFO 11:34:25 <br />
INFO 11:34:25 <br />
INFO 11:34:25 ----------------------------------- Platform -----------------------------------<br />
INFO 11:34:25 Java: JVM 1.8.0_121-b13 Memory: 2237M<br />
INFO 11:34:25 Language: en, Country: US<br />
INFO 11:34:25 Framework: Apache Software Foundation (1.8) <br />
INFO 11:34:25 OS: macosx (10.16)<br />
INFO 11:34:25 Processor: x86-64<br />
<br />
</pre><br />
<br />
There are several ways of setting the heap size depending on how you run Protege. Note that for 64 bit windows machines there is a but in InstallAnywhere that prevents the user from setting the heap size over something like 1.5G. So in this case you will have to set up the run.bat script method of starting Protege.<br />
<br />
__TOC__<br />
<br />
<br />
==== Start Protege by Protege.exe/Protege or by double-cliking on the Protege icon (Windows/Linux) ====<br />
<br />
Michael DeBellis wrote on 2021/12/22:<br />
<br />
<start><br />
Needing more memory for Desktop Protege is a common issue and there is a simple solution. In the main directory where you have Protege [version 5.5 in 2021] there should be a file called Protege.I4J.ini That file is what Protege looks at when it starts up to determine how much memory Java can allocate. If you edit that file in Notepad or some other lightweight text processor it should currently look like this:<br />
<br />
-Xms200M<br />
-Xmx500M<br />
-Xss16M<br />
<br />
Xmx is the one you want to edit (I would recommend you make a copy of the original file first). That specifies the maximum amount of memory Protege can use. Xms is the initial memory that will be allocated and Xss defines the increments used when allocating more memory. The main thing to keep in mind is not to allocate so much memory that it starts to limit the performance of other programs which of course depends on how much memory your desktop or laptop have. <br />
<end><br />
<br />
==== Start Protege by double-clicking on the Protege icon (Mac) ====<br />
<br />
If you run Protege on a Mac by double clicking an icon, you need to edit the Info.plist file that is hidden within that icon. Right click the icon (or ^-click for one button mouses) and click "show package contents". A new finder window will come up. Double click "Contents" and then "Info.plist". Traverse down the tree as follows: "Root" --> "Java" --> "JVMOptions". In JVMOptions edit the -Xmx line to indicate the correct memory usage. (Add the line <string>-Xmx2400M</string> if it's not there initially.)<br />
<key>JVMOptions</key><br />
<array><br />
<string>-Dapple.laf.useScreenMenuBar=true</string><br />
<string>-Xss16M</string><br />
<string>-Xms500M</string><br />
<string>-Xmx1400M</string><br />
<br />
<br />
==== Start Protege by double-clicking on the applescript file (Mac) ====<br />
<br />
If you run Protege on a Mac by double clicking the applescript file then you need to modify the -Xmx line in the script.<br />
<br />
<br />
==== Start Protege from the command line ====<br />
<br />
To run Protege from the command line, write in a terminal:<br />
<br />
.\run.sh<br />
<br />
(or, if on Windows, <code>run.bat</code>). You may change the heap size by editing the run script in a text editor, and change the value of the <code>-Xmx</code> argument. For example, to start with a 500MB heap size, use <code>-Xmx500M</code>. Read more on setting the heap size as an argument for generic Java applications [https://docs.oracle.com/javase/8/docs/technotes/tools/windows/java.html here] and [http://docs.oracle.com/javase/8/docs/technotes/guides/vm/gctuning/index.html here].<br />
<br />
Note that on Windows machines if you have installed the version of Protege that comes with its own jvm, you may need to change the path to java to jre\bin\java.exe. So for instance, to get 2G of heap space, you might change the Protege 5.5 run.bat file to be:<br />
<br />
<code>jre\bin\java -Xmx2G -Xms200M -Xss16M -XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot -DentityExpansionLimit=100000000 -Dlogback.configurationFile=conf/logback-win.xml -Dfile.encoding=utf-8 -Dorg.protege.plugin.dir=plugins -classpath bundles/guava.jar;bundles/logback-classic.jar;bundles/logback-core.jar;bundles/slf4j-api.jar;bin/org.apache.felix.main.jar;bin/maven-artifact.jar;bin/protege-launcher.jar org.protege.osgi.framework.Launcher %1<br />
</code><br />
<br />
<br />
[[Category:Protege documentation]]</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Setting_Heap_Size&diff=13806Setting Heap Size2022-02-18T04:39:02Z<p>Samsontu: </p>
<hr />
<div><span style="font-weight:bold;font-size:18px;">Setting the Heap Size</span><br />
<br />
<br />
<span style="font-weight:bold;font-size:16px;">Recommendations for setting the heap size (read first!)</span><br />
<br />
<br />
You must be careful about setting the heap size parameter. If you set it too low then you will get "out of memory" errors. If you set it too high then your system will hang or you will suffer poor performance because parts of the jvm will be swapped in and out of memory. A rule of thumb is that you should not set this parameter larger than about 80% of your free physical memory. On Windows XP machines you can determine your free physical memory from the Performance tab of the Task Manager application. On Mac machines, click the apple (upper left hand corner and "about this mac"). On Linux machines, you can use the wonderful proc filesystem and look at the meminfo "file".<br />
<br />
Boosting the heap size parameter will allow you to read in larger file-based projects. It will also improve the performance of the database back-end since more memory is available for caching.<br />
<br />
The most common source of very slow performance on older systems (or laptops) is having the heap size set too large. If your system does not have 100MB of free memory then even the Protege default value is too big and you should make it smaller (or buy more memory). <br />
<br />
The best way to know if you have succeeded in changing the memory settings is to look at the console when Protege starts up. Protege will print out the memory settings as they start. The console or the log during startup will look something like this:<br />
<pre><br />
INFO 11:34:25 ------------------------------------ Protege -----------------------------------<br />
INFO 11:34:25 Protege Desktop<br />
INFO 11:34:25 Version 5.5.0, Build <br />
INFO 11:34:25 <br />
INFO 11:34:25 <br />
INFO 11:34:25 ----------------------------------- Platform -----------------------------------<br />
INFO 11:34:25 Java: JVM 1.8.0_121-b13 Memory: 2237M<br />
INFO 11:34:25 Language: en, Country: US<br />
INFO 11:34:25 Framework: Apache Software Foundation (1.8) <br />
INFO 11:34:25 OS: macosx (10.16)<br />
INFO 11:34:25 Processor: x86-64<br />
<br />
</pre><br />
<br />
There are several ways of setting the heap size depending on how you run Protege. Note that for 64 bit windows machines there is a but in InstallAnywhere that prevents the user from setting the heap size over something like 1.5G. So in this case you will have to set up the run.bat script method of starting Protege.<br />
<br />
__TOC__<br />
<br />
<br />
==== Start Protege by Protege.exe/Protege or by double-cliking on the Protege icon (Windows/Linux) ====<br />
<br />
Michael DeBellis wrote on 2021/12/22:<br />
<br />
<start><br />
Needing more memory for Desktop Protege is a common issue and there is a simple solution. In the main directory where you have Protege [version 5.5 in 2021] there should be a file called Protege.I4J.ini That file is what Protege looks at when it starts up to determine how much memory Java can allocate. If you edit that file in Notepad or some other lightweight text processor it should currently look like this:<br />
<br />
-Xms200M<br />
-Xmx500M<br />
-Xss16M<br />
<br />
Xmx is the one you want to edit (I would recommend you make a copy of the original file first). That specifies the maximum amount of memory Protege can use. Xms is the initial memory that will be allocated and Xss defines the increments used when allocating more memory. The main thing to keep in mind is not to allocate so much memory that it starts to limit the performance of other programs which of course depends on how much memory your desktop or laptop have. <br />
<end><br />
<br />
==== Start Protege by double-clicking on the Protege icon (Mac) ====<br />
<br />
If you run Protege on a Mac by double clicking an icon, you need to edit the Info.plist file that is hidden within that icon. Right click the icon (or ^-click for one button mouses) and click "show package contents". A new finder window will come up. Double click "Contents" and then "Info.plist". Traverse down the tree as follows: "Root" --> "Java" --> "JVMOptions". In JVMOptions edit the -Xmx line to indicate the correct memory usage. (Add the line <string>-Xmx2400M</string> if it's not there initially.)<br />
<key>JVMOptions</key><br />
<array><br />
<string>-Dapple.laf.useScreenMenuBar=true</string><br />
<string>-Xss16M</string><br />
<string>-Xms500M</string><br />
<string>-Xmx1400M</string><br />
<br />
<br />
==== Start Protege by double-clicking on the applescript file (Mac) ====<br />
<br />
If you run Protege on a Mac by double clicking the applescript file then you need to modify the -Xmx line in the script.<br />
<br />
<br />
==== Start Protege from the command line ====<br />
<br />
To run Protege from the command line, write in a terminal:<br />
<br />
.\run.sh<br />
<br />
(or, if on Windows, <code>run.bat</code>). You may change the heap size by editing the run script in a text editor, and change the value of the <code>-Xmx</code> argument. For example, to start with a 500MB heap size, use <code>-Xmx500M</code>. Read more on setting the heap size as an argument for generic Java applications [https://docs.oracle.com/javase/8/docs/technotes/tools/windows/java.html here] and [http://docs.oracle.com/javase/8/docs/technotes/guides/vm/gctuning/index.html here].<br />
<br />
Note that on Windows machines if you have installed the version of Protege that comes with its own jvm, you may need to change the path to java to jre\bin\java.exe. So for instance, to get 2G of heap space, you might change the Protege 4.2 run.bat file to be:<br />
<br />
<code>jre\bin\java.exe -Xmx2G -Dlog4j.configuration=file:log4j.xml -DentityExpansionLimit=100000000 -Dfile.encoding=utf-8 -Dorg.protege.plugin.dir=plugins -classpath bin/felix.jar;bin/ProtegeLauncher.jar org.protege.osgi.framework.Launcher</code><br />
<br />
<br />
[[Category:Protege documentation]]</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Protege-OWL_4_FAQ&diff=13805Protege-OWL 4 FAQ2022-02-17T23:50:22Z<p>Samsontu: </p>
<hr />
<div>__TOC__<br /><br />
<br />
== Protege Desktop Frequently Asked Questions ==<br />
<br />
<span style="color:red; font-weight:bold;">This FAQ is specific to Protege Desktop, versions 4, 5 and above.</span><br />
<br />
If you're working with older versions of Protege, you might find the following alternative FAQs helpful:<br />
<br />
* [[Protege-OWL_3_FAQ|Protege-OWL 3.x FAQ]]<br />
* [http://protege.stanford.edu/doc/faq.html Protege-Frames FAQ]<br />
<br />
=== How do I install Protege Desktop? ===<br />
Protege Desktop is [http://protege.stanford.edu/products.php#desktop-protege available for download] from the main Protege website. <br />
<br />
=== Where can I find user documentation for Protege Desktop? ===<br />
See [http://protegeproject.github.io/protege/ Prot&eacute;g&eacute; 5 Documentation].<br />
Also refer to the [[Protege4UserDocs#Protege-OWL_Editor|Protege documentation page]] on this wiki for a list of older documentation that uses Prot&eacute;g&eacute; 4 user interface but are still substantially correct.<br />
<br />
=== Where do I ask questions and report bugs? ===<br />
Please post comments, questions, and bug reports on the [http://mailman.stanford.edu/mailman/listinfo/protege-user protege-user mailing list]. Note that you must be subscribed to the list in order to post messages. If you have difficulties subscribing or unsubscribing from protege-user, please contact the [mailto:protege-user-owner@lists.stanford.edu list owners].<br />
<br />
=== Where can I look at a list known bugs and feature requests? ===<br />
<br />
Visit our issue tracker on GitHub: https://github.com/protegeproject/protege/issues?state=open.<br />
<br />
=== Why do I get a message about a damaged installer file on the Mac? ===<br />
OS X users might see the following error message when trying to install Protege Desktop:<br />
<br />
<br />
[[Image:Mac_damaged_installer_error_msg.png]]<br />
<br />
<br />
This is a misleading error message from Apple's [http://support.apple.com/kb/ht5290 Gatekeeper] software. By default, Gatekeeper is configured to only allow download and installation of applications from the Mac App Store and identified developers. The Protege Desktop software does not yet carry "identified developer" status. To successfully install Protege Desktop, navigate to Apple menu | System Preferences… | Security & Privacy | General tab, and select "Anywhere" from "Allow applications downloaded from".<br />
<br />
=== Why am I getting "An error related to DOT has occurred" when trying to use the OWLViz plug-in? ===<br />
If you see this error when trying to use OWLViz, it means that you have not completed some of the necessary steps to configure this plug-in. Complete documentation for fixing this error is available in the [http://protegewiki.stanford.edu/index.php/OWLViz#Troubleshooting troubleshooting section] of the OWLViz documentation.<br />
<br />
=== How do I change the name of an entity (class, property, individual) in my ontology? ===<br />
Select the Refactor | Change entity URI... menu item. In the resulting Change entity URI dialog box, enter the new name in the text box, and click the OK button.<br />
<br />
=== Why does my ontology contain classes named Error1, Error2, ...? ===<br />
See the [[Protege4ErrorClasses|Error Classes]] page for a description of this new OWL API feature.<br />
<br />
=== How do I change the allocated heap memory when I get the Java out-of-memory error? ===<br />
See the [[Setting_Heap_Size]] page for instructions.<br />
<br />
=== How do I edit/use SWRL rules in Protege ===<br />
* Create a new tab (Window -> Views -> Create new tab...) called something like Rules, SWRL or whatever you prefer [OPTIONAL]<br />
* Select the Window -> Views -> Ontology views -> Rules menu and drop the "Rules" view in a tab (for example the one created in the previous step)<br />
* Different reasoners have different level of support for rules. Pellet has the best support for SWRL rules. If you don't see Pellet listed in your Reasoner menu, install it (Open Files -> Preferences, select Plugins tab, press on "Check for downloads now" button, select and install Pellet) <br />
* In the Reasoner menu select the the Pellet reasoner [IMPORTANT]<br />
* View/Create/Edit/Delete SWRL rules in the "Rules" view<br />
* Start (Reasoner -> Start reasoner) or synchronize (Reasoner -> Synchronize reasoner) the reasoner (you can also do it with CTRL+R or COMMAND+R on Mac)<br />
* See results of the executed rules in you other views<br />
<br />
=== What are the pros and cons of DL Query, SPARQL (with OWL entailment regime), and SQWRL===<br />
A DL Query is a OWL class expression. It<br />
* Returns results that can be superclasses, subclasses, or individuals of the class expression.<br />
* Has compact notation<br />
* Cannot use variables, therefore cannot compare values from different properties e.g., (forall all individuals ?x of class C where ?x.length = ?x.width)<br />
* Has limited sets of operators (e.g., can use regular expressions on strings but cannot do arithmetic)<br />
* Uses open-world assumption<br />
* Resolves queries relative to import closure, does not support federated queries<br />
* Is supported by any OWL reasoning system (Protege has GUI for DL queries)<br />
<br />
SPARQL query is a graph pattern. It<br />
* Can match against anything against graph patterns.<br />
* Has a rich set of operators and functions on numbers, strings, date/time, and terms<br />
* Is widely supported (although not all SPARQL engine support OWL2 entailment regime)<br />
* Can be resolved against relational databases with mappings (e.g., Ontop)<br />
* Supports federated queries across the net<br />
* Can work with OWL ontology because of formalized OWL to RDF mapping. Complex class expressions have very verbose RDF representation.<br />
<br />
SQWRL is an extension of OWL/SWRL. It<br />
* Natively understands OWL<br />
* Allows you to query for individuals only<br />
* Has an extensible collection of built-ins (including the ability to do arithmetic)<br />
* Has set operators that “close the world”<br />
* Allows comparison of values of different properties on the same individual<br />
* Is supported by Protege only<br />
* Does not support federated queries across the net</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Protege-OWL_4_FAQ&diff=13804Protege-OWL 4 FAQ2022-02-17T23:44:21Z<p>Samsontu: </p>
<hr />
<div>__TOC__<br /><br />
<br />
== Protege Desktop Frequently Asked Questions ==<br />
<br />
<span style="color:red; font-weight:bold;">This FAQ is specific to Protege Desktop, versions 4, 5 and above.</span><br />
<br />
If you're working with older versions of Protege, you might find the following alternative FAQs helpful:<br />
<br />
* [[Protege-OWL_3_FAQ|Protege-OWL 3.x FAQ]]<br />
* [http://protege.stanford.edu/doc/faq.html Protege-Frames FAQ]<br />
<br />
=== How do I install Protege Desktop? ===<br />
Protege Desktop is [http://protege.stanford.edu/products.php#desktop-protege available for download] from the main Protege website. <br />
<br />
=== Where can I find user documentation for Protege Desktop? ===<br />
See [http://protegeproject.github.io/protege/ Prot&eacute;g&eacute; 5 Documentation].<br />
Also refer to the [[Protege4UserDocs#Protege-OWL_Editor|Protege documentation page]] on this wiki for a list of older documentation that uses Prot&eacute;g&eacute; 4 user interface but are still substantially correct.<br />
<br />
=== Where do I ask questions and report bugs? ===<br />
Please post comments, questions, and bug reports on the [http://mailman.stanford.edu/mailman/listinfo/protege-user protege-user mailing list]. Note that you must be subscribed to the list in order to post messages. If you have difficulties subscribing or unsubscribing from protege-user, please contact the [mailto:protege-user-owner@lists.stanford.edu list owners].<br />
<br />
=== Where can I look at a list known bugs and feature requests? ===<br />
<br />
Visit our issue tracker on GitHub: https://github.com/protegeproject/protege/issues?state=open.<br />
<br />
=== Why do I get a message about a damaged installer file on the Mac? ===<br />
OS X users might see the following error message when trying to install Protege Desktop:<br />
<br />
<br />
[[Image:Mac_damaged_installer_error_msg.png]]<br />
<br />
<br />
This is a misleading error message from Apple's [http://support.apple.com/kb/ht5290 Gatekeeper] software. By default, Gatekeeper is configured to only allow download and installation of applications from the Mac App Store and identified developers. The Protege Desktop software does not yet carry "identified developer" status. To successfully install Protege Desktop, navigate to Apple menu | System Preferences… | Security & Privacy | General tab, and select "Anywhere" from "Allow applications downloaded from".<br />
<br />
=== Why am I getting "An error related to DOT has occurred" when trying to use the OWLViz plug-in? ===<br />
If you see this error when trying to use OWLViz, it means that you have not completed some of the necessary steps to configure this plug-in. Complete documentation for fixing this error is available in the [http://protegewiki.stanford.edu/index.php/OWLViz#Troubleshooting troubleshooting section] of the OWLViz documentation.<br />
<br />
=== How do I change the name of an entity (class, property, individual) in my ontology? ===<br />
Select the Refactor | Change entity URI... menu item. In the resulting Change entity URI dialog box, enter the new name in the text box, and click the OK button.<br />
<br />
=== Why does my ontology contain classes named Error1, Error2, ...? ===<br />
See the [[Protege4ErrorClasses|Error Classes]] page for a description of this new OWL API feature.<br />
<br />
=== How do I change the allocated heap memory when I get the Java out-of-memory error? ===<br />
See the [[Setting_Heap_Size]] page for instructions.<br />
<br />
=== How do I edit/use SWRL rules in Protege ===<br />
* Create a new tab (Window -> Views -> Create new tab...) called something like Rules, SWRL or whatever you prefer [OPTIONAL]<br />
* Select the Window -> Views -> Ontology views -> Rules menu and drop the "Rules" view in a tab (for example the one created in the previous step)<br />
* Different reasoners have different level of support for rules. Pellet has the best support for SWRL rules. If you don't see Pellet listed in your Reasoner menu, install it (Open Files -> Preferences, select Plugins tab, press on "Check for downloads now" button, select and install Pellet) <br />
* In the Reasoner menu select the the Pellet reasoner [IMPORTANT]<br />
* View/Create/Edit/Delete SWRL rules in the "Rules" view<br />
* Start (Reasoner -> Start reasoner) or synchronize (Reasoner -> Synchronize reasoner) the reasoner (you can also do it with CTRL+R or COMMAND+R on Mac)<br />
* See results of the execurted rules in you other views<br />
<br />
=== What are the pros and cons of DL Query, SPARQL (with OWL entailment regime), and SQWRL===<br />
A DL Query is a OWL class expression. It<br />
* Returns results that can be superclasses, subclasses, or individuals of the class expression.<br />
* Has compact notation<br />
* Cannot use variables, therefore cannot compare values from different properties e.g., (forall all individuals ?x of class C where ?x.length = ?x.width)<br />
* Has limited sets of operators (e.g., can use regular expressions on strings but cannot do arithmetic)<br />
* Uses open-world assumption<br />
* Resolves queries relative to import closure, does not support federated queries<br />
* Is supported by any OWL reasoning system (Protege has GUI for DL queries)<br />
<br />
SPARQL query is a graph pattern. It<br />
* Can match against anything against graph patterns.<br />
* Has a rich set of operators and functions on numbers, strings, date/time, and terms<br />
* Is widely supported (although not all SPARQL engine support OWL2 entailment regime)<br />
* Can be resolved against relational databases with mappings (e.g., Ontop)<br />
* Supports federated queries across the net<br />
* Can work with OWL ontology because of formalized OWL to RDF mapping. Complex class expressions have very verbose RDF representation.<br />
<br />
SQWRL is an extension of OWL/SWRL. It<br />
* Natively understands OWL<br />
* Allows you to query for individuals only<br />
* Has an extensible collection of built-ins (including the ability to do arithmetic)<br />
* Has set operators that “close the world”<br />
* Allows comparison of values of different properties on the same individual<br />
* Is supported by Protege only<br />
* Does not support federated queries across the net</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Protege-OWL_4_FAQ&diff=13803Protege-OWL 4 FAQ2022-02-17T23:43:19Z<p>Samsontu: </p>
<hr />
<div>__TOC__<br /><br />
<br />
== Protege Desktop Frequently Asked Questions ==<br />
<br />
<span style="color:red; font-weight:bold;">This FAQ is specific to Protege Desktop, versions 4, 5 and above.</span><br />
<br />
If you're working with older versions of Protege, you might find the following alternative FAQs helpful:<br />
<br />
* [[Protege-OWL_3_FAQ|Protege-OWL 3.x FAQ]]<br />
* [http://protege.stanford.edu/doc/faq.html Protege-Frames FAQ]<br />
<br />
=== How do I install Protege Desktop? ===<br />
Protege Desktop is [http://protege.stanford.edu/products.php#desktop-protege available for download] from the main Protege website. <br />
<br />
=== Where can I find user documentation for Protege Desktop? ===<br />
See [http://protegeproject.github.io/protege/ Prot&eacute;g&eacute; 5 Documentation]<br />
Also refer to the [[Protege4UserDocs#Protege-OWL_Editor|Protege documentation page]] on this wiki for a list of older documentation that uses Prot&eacute;g&eacute; user interface but are still substantially correct.<br />
<br />
=== Where do I ask questions and report bugs? ===<br />
Please post comments, questions, and bug reports on the [http://mailman.stanford.edu/mailman/listinfo/protege-user protege-user mailing list]. Note that you must be subscribed to the list in order to post messages. If you have difficulties subscribing or unsubscribing from protege-user, please contact the [mailto:protege-user-owner@lists.stanford.edu list owners].<br />
<br />
=== Where can I look at a list known bugs and feature requests? ===<br />
<br />
Visit our issue tracker on GitHub: https://github.com/protegeproject/protege/issues?state=open.<br />
<br />
=== Why do I get a message about a damaged installer file on the Mac? ===<br />
OS X users might see the following error message when trying to install Protege Desktop:<br />
<br />
<br />
[[Image:Mac_damaged_installer_error_msg.png]]<br />
<br />
<br />
This is a misleading error message from Apple's [http://support.apple.com/kb/ht5290 Gatekeeper] software. By default, Gatekeeper is configured to only allow download and installation of applications from the Mac App Store and identified developers. The Protege Desktop software does not yet carry "identified developer" status. To successfully install Protege Desktop, navigate to Apple menu | System Preferences… | Security & Privacy | General tab, and select "Anywhere" from "Allow applications downloaded from".<br />
<br />
=== Why am I getting "An error related to DOT has occurred" when trying to use the OWLViz plug-in? ===<br />
If you see this error when trying to use OWLViz, it means that you have not completed some of the necessary steps to configure this plug-in. Complete documentation for fixing this error is available in the [http://protegewiki.stanford.edu/index.php/OWLViz#Troubleshooting troubleshooting section] of the OWLViz documentation.<br />
<br />
=== How do I change the name of an entity (class, property, individual) in my ontology? ===<br />
Select the Refactor | Change entity URI... menu item. In the resulting Change entity URI dialog box, enter the new name in the text box, and click the OK button.<br />
<br />
=== Why does my ontology contain classes named Error1, Error2, ...? ===<br />
See the [[Protege4ErrorClasses|Error Classes]] page for a description of this new OWL API feature.<br />
<br />
=== How do I change the allocated heap memory when I get the Java out-of-memory error? ===<br />
See the [[Setting_Heap_Size]] page for instructions.<br />
<br />
=== How do I edit/use SWRL rules in Protege ===<br />
* Create a new tab (Window -> Views -> Create new tab...) called something like Rules, SWRL or whatever you prefer [OPTIONAL]<br />
* Select the Window -> Views -> Ontology views -> Rules menu and drop the "Rules" view in a tab (for example the one created in the previous step)<br />
* Different reasoners have different level of support for rules. Pellet has the best support for SWRL rules. If you don't see Pellet listed in your Reasoner menu, install it (Open Files -> Preferences, select Plugins tab, press on "Check for downloads now" button, select and install Pellet) <br />
* In the Reasoner menu select the the Pellet reasoner [IMPORTANT]<br />
* View/Create/Edit/Delete SWRL rules in the "Rules" view<br />
* Start (Reasoner -> Start reasoner) or synchronize (Reasoner -> Synchronize reasoner) the reasoner (you can also do it with CTRL+R or COMMAND+R on Mac)<br />
* See results of the execurted rules in you other views<br />
<br />
=== What are the pros and cons of DL Query, SPARQL (with OWL entailment regime), and SQWRL===<br />
A DL Query is a OWL class expression. It<br />
* Returns results that can be superclasses, subclasses, or individuals of the class expression.<br />
* Has compact notation<br />
* Cannot use variables, therefore cannot compare values from different properties e.g., (forall all individuals ?x of class C where ?x.length = ?x.width)<br />
* Has limited sets of operators (e.g., can use regular expressions on strings but cannot do arithmetic)<br />
* Uses open-world assumption<br />
* Resolves queries relative to import closure, does not support federated queries<br />
* Is supported by any OWL reasoning system (Protege has GUI for DL queries)<br />
<br />
SPARQL query is a graph pattern. It<br />
* Can match against anything against graph patterns.<br />
* Has a rich set of operators and functions on numbers, strings, date/time, and terms<br />
* Is widely supported (although not all SPARQL engine support OWL2 entailment regime)<br />
* Can be resolved against relational databases with mappings (e.g., Ontop)<br />
* Supports federated queries across the net<br />
* Can work with OWL ontology because of formalized OWL to RDF mapping. Complex class expressions have very verbose RDF representation.<br />
<br />
SQWRL is an extension of OWL/SWRL. It<br />
* Natively understands OWL<br />
* Allows you to query for individuals only<br />
* Has an extensible collection of built-ins (including the ability to do arithmetic)<br />
* Has set operators that “close the world”<br />
* Allows comparison of values of different properties on the same individual<br />
* Is supported by Protege only<br />
* Does not support federated queries across the net</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Main_Page&diff=13802Main Page2022-02-17T23:30:04Z<p>Samsontu: </p>
<hr />
<div>__NOTOC__<br />
= <span style="color:#2c3e50;"> Welcome to the Prot&eacute;g&eacute; wiki! </span> =<br />
<br />
[[File:WP-classes.png|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[WebProtege|WebProt&eacute;g&eacute;]] - a powerful collaborative ontology development environment for the Web </span>]]<br />
<br />
[[File:Protege-OWL.jpg|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[Protege4UserDocs|Prot&eacute;g&eacute; Desktop]] - a fully-fledged OWL 2 ontology editor for the desktops</span>]]<br />
<br />
[https://protege.stanford.edu Prot&eacute;g&eacute;] 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. <br />
<br />
''' Quick links: [https://webprotege.stanford.edu WebProt&eacute;g&eacute; server], Prot&eacute;g&eacute; Desktop [https://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], [https://protege.stanford.edu Prot&eacute;g&eacute; website] '''<br />
<br />
= <span style="color:#2c3e50;"> User Documentation </span>=<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
* [[WebProtege|Overview]]<br />
* [[WebProtegeUsersGuide|User's Guide]]<br />
* [https://github.com/protegeproject/webprotege/wiki/WebProtégé-4.0.0-beta-x-Installation Administrator's Guide] - download and installation instructions<br />
* Use WebProt&eacute;g&eacute; now on our Stanford-hosted server: http://webprotege.stanford.edu<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [http://protegeproject.github.io/protege/ Prot&eacute;g&eacute; Desktop documentation] ([https://github.com/protegeproject/protege-distribution/releases release notes], [http://protegeproject.github.io/protege/installation/ installation instructions], [http://protege.stanford.edu/products.php#desktop-protege Protege Desktop download], [[Protege_Desktop_Old_Versions|older Protege releases download]])<br />
* [http://protegeproject.github.io/protege/views/ Views], [http://protegeproject.github.io/protege/menus/ Menus], [http://protegeproject.github.io/protege/class-expression-syntax/ Class Expression Syntax] - a short guide to some of the desktop Prot&eacute;g&eacute; interface components<br />
* [[Protege3UserDocs|Older Prot&eacute;g&eacute; releases documentation (version 3.x)]]<br />
* [[Protege-OWL_4_FAQ|Frequently Asked Questions (FAQ)]]<br />
<br />
=== <span style="color:#2c3e50;"> Tutorials and Getting Started</span> ===<br />
* [http://protegeproject.github.io/protege/getting-started/ Getting started with the Protege Desktop editor] <br />
Tutorials<br />
* [https://www.michaeldebellis.com/post/new-protege-pizza-tutorial Michael DeBellis's updated Prot&eacute;g&eacute; Pizza Tutorial]<br />
* [http://owl.cs.manchester.ac.uk/publications/talks-and-tutorials/protg-owl-tutorial/ The original Prot&eacute;g&eacute; OWL Tutorial: A step-by-step guide to modeling in OWL using the Prot&eacute;g&eacute; OWL tools]<br />
<br />
Background Information<br />
* [http://protege.stanford.edu/publications/ontology_development/ontology101.html Ontology Development 101: A Guide to creating your first ontology]<br />
* [http://www.cs.man.ac.uk/~stevensr/menupages/background.php Brief introduction to ontologies], by Robert Stevens<br />
* Semantic Web Best Practices and Deployment Working Group's [http://www.w3.org/2001/sw/BestPractices/Tutorials Semantic Web Tutorials] page<br />
* [http://arxiv.org/abs/1201.4089 A Description Logic Primer]<br />
<br />
Older documentation, illustrated with Prot&eacute;g&eacute; 4 user interface, but substantially correct.<br />
* [[Pr4_UG | Protege Desktop User's Guide]] - a guide on how to use Protege to create, edit, and inspect ontologies<br />
* [[Protege4Pizzas10Minutes | Pizzas in 10 minutes: A demo of modeling shortcuts]] - a quickstart guide to creating your first OWL ontology<br />
<br />
= <span style="color:#2c3e50;"> Developer Documentation </span> =<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
<br />
Please see the [https://github.com/protegeproject/webprotege WebProt&eacute;g&eacute; GitHub page]<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [[Protege5DevDocs|Prot&eacute;g&eacute; Desktop 5.x]]<br />
* [[Protege4DevDocs|Prot&eacute;g&eacute; Desktop 4.x]]<br />
* [[Protege3DevDocs|Prot&eacute;g&eacute; Desktop 3.x]]<br />
<br />
* [[ProtegeQAGuide|Guide to Quality Assurance]]<br />
<br />
<br />
= <span style="color:#2c3e50;"> Download and Support </span> =<br />
<br />
To download Prot&eacute;g&eacute; or WebProt&eacute;g&eacute; please visit our [http://protege.stanford.edu homepage]. To use the WebProt&eacute;g&eacute; server hosted at Stanford, please go to: http://webprotege.stanford.edu. <br />
<br />
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].<br />
<br />
Follow our [http://www.youtube.com/user/TheProtegeProject YouTube channel] featuring screencasts showing different features of Prot&eacute;g&eacute; and WebProt&eacute;g&eacute;.<br />
<br />
<br />
= <span style="color:#2c3e50;"> Wiki Help </span> =<br />
If you are new to using a Wiki, please see the [[Help:Contents|Help page]] page for links to User's Guides, etc. <br />
<br />
The [[Help:Contents|Help page]] also has suggestions for where to find help with using the Prot&eacute;g&eacute; application.</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Main_Page&diff=13801Main Page2022-02-17T23:29:36Z<p>Samsontu: /* Tutorials and Getting Started */</p>
<hr />
<div>__NOTOC__<br />
= <span style="color:#2c3e50;"> Welcome to the Prot&eacute;g&eacute; wiki! </span> =<br />
<br />
[[File:WP-classes.png|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[WebProtege|WebProt&eacute;g&eacute;]] - a powerful collaborative ontology development environment for the Web </span>]]<br />
<br />
[[File:Protege-OWL.jpg|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[Protege4UserDocs|Prot&eacute;g&eacute; Desktop]] - a fully-fledged OWL 2 ontology editor for the desktops</span>]]<br />
<br />
[https://protege.stanford.edu Prot&eacute;g&eacute;] 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. <br />
<br />
''' Quick links: [https://webprotege.stanford.edu WebProt&eacute;g&eacute; server], Prot&eacute;g&eacute; Desktop [https://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], [https://protege.stanford.edu Prot&eacute;g&eacute; website] '''<br />
<br />
= <span style="color:#2c3e50;"> User Documentation </span>=<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
* [[WebProtege|Overview]]<br />
* [[WebProtegeUsersGuide|User's Guide]]<br />
* [https://github.com/protegeproject/webprotege/wiki/WebProtégé-4.0.0-beta-x-Installation Administrator's Guide] - download and installation instructions<br />
* Use WebProt&eacute;g&eacute; now on our Stanford-hosted server: http://webprotege.stanford.edu<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [http://protegeproject.github.io/protege/ Prot&eacute;g&eacute; Desktop documentation] ([https://github.com/protegeproject/protege-distribution/releases release notes], [http://protegeproject.github.io/protege/installation/ installation instructions], [http://protege.stanford.edu/products.php#desktop-protege Protege Desktop download], [[Protege_Desktop_Old_Versions|older Protege releases download]])<br />
* [http://protegeproject.github.io/protege/views/ Views], [http://protegeproject.github.io/protege/menus/ Menus], [http://protegeproject.github.io/protege/class-expression-syntax/ Class Expression Syntax] - a short guide to some of the desktop Prot&eacute;g&eacute; interface components<br />
* [[Protege3UserDocs|Older Prot&eacute;g&eacute; releases documentation (version 3.x)]]<br />
* [[Protege-OWL_4_FAQ|Frequently Asked Questions (FAQ)]]<br />
<br />
<br />
=== <span style="color:#2c3e50;"> Tutorials and Getting Started</span> ===<br />
* [http://protegeproject.github.io/protege/getting-started/ Getting started with the Protege Desktop editor] <br />
Tutorials<br />
* [https://www.michaeldebellis.com/post/new-protege-pizza-tutorial Michael DeBellis's updated Prot&eacute;g&eacute; Pizza Tutorial]<br />
* [http://owl.cs.manchester.ac.uk/publications/talks-and-tutorials/protg-owl-tutorial/ The original Prot&eacute;g&eacute; OWL Tutorial: A step-by-step guide to modeling in OWL using the Prot&eacute;g&eacute; OWL tools]<br />
<br />
Background Information<br />
* [http://protege.stanford.edu/publications/ontology_development/ontology101.html Ontology Development 101: A Guide to creating your first ontology]<br />
* [http://www.cs.man.ac.uk/~stevensr/menupages/background.php Brief introduction to ontologies], by Robert Stevens<br />
* Semantic Web Best Practices and Deployment Working Group's [http://www.w3.org/2001/sw/BestPractices/Tutorials Semantic Web Tutorials] page<br />
* [http://arxiv.org/abs/1201.4089 A Description Logic Primer]<br />
<br />
Older documentation, illustrated with Prot&eacute;g&eacute; 4 user interface, but substantially correct.<br />
* [[Pr4_UG | Protege Desktop User's Guide]] - a guide on how to use Protege to create, edit, and inspect ontologies<br />
* [[Protege4Pizzas10Minutes | Pizzas in 10 minutes: A demo of modeling shortcuts]] - a quickstart guide to creating your first OWL ontology<br />
<br />
= <span style="color:#2c3e50;"> Developer Documentation </span> =<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
<br />
Please see the [https://github.com/protegeproject/webprotege WebProt&eacute;g&eacute; GitHub page]<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [[Protege5DevDocs|Prot&eacute;g&eacute; Desktop 5.x]]<br />
* [[Protege4DevDocs|Prot&eacute;g&eacute; Desktop 4.x]]<br />
* [[Protege3DevDocs|Prot&eacute;g&eacute; Desktop 3.x]]<br />
<br />
* [[ProtegeQAGuide|Guide to Quality Assurance]]<br />
<br />
<br />
= <span style="color:#2c3e50;"> Download and Support </span> =<br />
<br />
To download Prot&eacute;g&eacute; or WebProt&eacute;g&eacute; please visit our [http://protege.stanford.edu homepage]. To use the WebProt&eacute;g&eacute; server hosted at Stanford, please go to: http://webprotege.stanford.edu. <br />
<br />
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].<br />
<br />
Follow our [http://www.youtube.com/user/TheProtegeProject YouTube channel] featuring screencasts showing different features of Prot&eacute;g&eacute; and WebProt&eacute;g&eacute;.<br />
<br />
<br />
= <span style="color:#2c3e50;"> Wiki Help </span> =<br />
If you are new to using a Wiki, please see the [[Help:Contents|Help page]] page for links to User's Guides, etc. <br />
<br />
The [[Help:Contents|Help page]] also has suggestions for where to find help with using the Prot&eacute;g&eacute; application.</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Main_Page&diff=13800Main Page2022-02-17T23:29:12Z<p>Samsontu: /* User Documentation */</p>
<hr />
<div>__NOTOC__<br />
= <span style="color:#2c3e50;"> Welcome to the Prot&eacute;g&eacute; wiki! </span> =<br />
<br />
[[File:WP-classes.png|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[WebProtege|WebProt&eacute;g&eacute;]] - a powerful collaborative ontology development environment for the Web </span>]]<br />
<br />
[[File:Protege-OWL.jpg|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[Protege4UserDocs|Prot&eacute;g&eacute; Desktop]] - a fully-fledged OWL 2 ontology editor for the desktops</span>]]<br />
<br />
[https://protege.stanford.edu Prot&eacute;g&eacute;] 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. <br />
<br />
''' Quick links: [https://webprotege.stanford.edu WebProt&eacute;g&eacute; server], Prot&eacute;g&eacute; Desktop [https://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], [https://protege.stanford.edu Prot&eacute;g&eacute; website] '''<br />
<br />
= <span style="color:#2c3e50;"> User Documentation </span>=<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
* [[WebProtege|Overview]]<br />
* [[WebProtegeUsersGuide|User's Guide]]<br />
* [https://github.com/protegeproject/webprotege/wiki/WebProtégé-4.0.0-beta-x-Installation Administrator's Guide] - download and installation instructions<br />
* Use WebProt&eacute;g&eacute; now on our Stanford-hosted server: http://webprotege.stanford.edu<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [http://protegeproject.github.io/protege/ Prot&eacute;g&eacute; Desktop documentation] ([https://github.com/protegeproject/protege-distribution/releases release notes], [http://protegeproject.github.io/protege/installation/ installation instructions], [http://protege.stanford.edu/products.php#desktop-protege Protege Desktop download], [[Protege_Desktop_Old_Versions|older Protege releases download]])<br />
* [http://protegeproject.github.io/protege/views/ Views], [http://protegeproject.github.io/protege/menus/ Menus], [http://protegeproject.github.io/protege/class-expression-syntax/ Class Expression Syntax] - a short guide to some of the desktop Prot&eacute;g&eacute; interface components<br />
* [[Protege3UserDocs|Older Prot&eacute;g&eacute; releases documentation (version 3.x)]]<br />
* [[Protege-OWL_4_FAQ|Frequently Asked Questions (FAQ)]]<br />
<br />
<br />
=== <span style="color:#2c3e50;"> Tutorials and Getting Started</span> ===<br />
* [http://protegeproject.github.io/protege/getting-started/ Getting started with the Protege Desktop editor] <br />
Tutorials<br />
* [https://www.michaeldebellis.com/post/new-protege-pizza-tutorial Michael DeBellis's updated Prot&eacute;g&eacute; Pizza Tutorial]<br />
* [http://owl.cs.manchester.ac.uk/publications/talks-and-tutorials/protg-owl-tutorial/ The original Prot&eacute;g&eacute; OWL Tutorial: A step-by-step guide to modeling in OWL using the Prot&eacute;g&eacute; OWL tools]<br />
<br />
Background Information<br />
* [http://protege.stanford.edu/publications/ontology_development/ontology101.html Ontology Development 101: A Guide to creating your first ontology]<br />
* [http://www.cs.man.ac.uk/~stevensr/menupages/background.php Brief introduction to ontologies], by Robert Stevens<br />
* Semantic Web Best Practices and Deployment Working Group's [http://www.w3.org/2001/sw/BestPractices/Tutorials Semantic Web Tutorials] page<br />
* [http://arxiv.org/abs/1201.4089 A Description Logic Primer]<br />
<br />
Older documentation, illustrated with Prot&eacute;g&eacute; user interface, but substantially correct.<br />
* [[Pr4_UG | Protege Desktop User's Guide]] - a guide on how to use Protege to create, edit, and inspect ontologies<br />
* [[Protege4Pizzas10Minutes | Pizzas in 10 minutes: A demo of modeling shortcuts]] - a quickstart guide to creating your first OWL ontology<br />
<br />
= <span style="color:#2c3e50;"> Developer Documentation </span> =<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
<br />
Please see the [https://github.com/protegeproject/webprotege WebProt&eacute;g&eacute; GitHub page]<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [[Protege5DevDocs|Prot&eacute;g&eacute; Desktop 5.x]]<br />
* [[Protege4DevDocs|Prot&eacute;g&eacute; Desktop 4.x]]<br />
* [[Protege3DevDocs|Prot&eacute;g&eacute; Desktop 3.x]]<br />
<br />
* [[ProtegeQAGuide|Guide to Quality Assurance]]<br />
<br />
<br />
= <span style="color:#2c3e50;"> Download and Support </span> =<br />
<br />
To download Prot&eacute;g&eacute; or WebProt&eacute;g&eacute; please visit our [http://protege.stanford.edu homepage]. To use the WebProt&eacute;g&eacute; server hosted at Stanford, please go to: http://webprotege.stanford.edu. <br />
<br />
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].<br />
<br />
Follow our [http://www.youtube.com/user/TheProtegeProject YouTube channel] featuring screencasts showing different features of Prot&eacute;g&eacute; and WebProt&eacute;g&eacute;.<br />
<br />
<br />
= <span style="color:#2c3e50;"> Wiki Help </span> =<br />
If you are new to using a Wiki, please see the [[Help:Contents|Help page]] page for links to User's Guides, etc. <br />
<br />
The [[Help:Contents|Help page]] also has suggestions for where to find help with using the Prot&eacute;g&eacute; application.</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Main_Page&diff=13799Main Page2022-02-17T23:17:26Z<p>Samsontu: </p>
<hr />
<div>__NOTOC__<br />
= <span style="color:#2c3e50;"> Welcome to the Prot&eacute;g&eacute; wiki! </span> =<br />
<br />
[[File:WP-classes.png|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[WebProtege|WebProt&eacute;g&eacute;]] - a powerful collaborative ontology development environment for the Web </span>]]<br />
<br />
[[File:Protege-OWL.jpg|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[Protege4UserDocs|Prot&eacute;g&eacute; Desktop]] - a fully-fledged OWL 2 ontology editor for the desktops</span>]]<br />
<br />
[https://protege.stanford.edu Prot&eacute;g&eacute;] 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. <br />
<br />
''' Quick links: [https://webprotege.stanford.edu WebProt&eacute;g&eacute; server], Prot&eacute;g&eacute; Desktop [https://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], [https://protege.stanford.edu Prot&eacute;g&eacute; website] '''<br />
<br />
= <span style="color:#2c3e50;"> User Documentation </span>=<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
* [[WebProtege|Overview]]<br />
* [[WebProtegeUsersGuide|User's Guide]]<br />
* [https://github.com/protegeproject/webprotege/wiki/WebProtégé-4.0.0-beta-x-Installation Administrator's Guide] - download and installation instructions<br />
* Use WebProt&eacute;g&eacute; now on our Stanford-hosted server: http://webprotege.stanford.edu<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [http://protegeproject.github.io/protege/ Prot&eacute;g&eacute; Desktop documentation] ([https://github.com/protegeproject/protege-distribution/releases release notes], [http://protegeproject.github.io/protege/installation/ installation instructions], [http://protege.stanford.edu/products.php#desktop-protege Protege Desktop download], [[Protege_Desktop_Old_Versions|older Protege releases download]])<br />
* [http://protegeproject.github.io/protege/views/ Views], [http://protegeproject.github.io/protege/menus/ Menus], [http://protegeproject.github.io/protege/class-expression-syntax/ Class Expression Syntax] - a short guide to some of the desktop Prot&eacute;g&eacute; interface components<br />
* [[Protege3UserDocs|Older Prot&eacute;g&eacute; releases documentation (version 3.x)]]<br />
* [[Protege-OWL_4_FAQ|Frequently Asked Questions (FAQ)]]<br />
<br />
<br />
=== <span style="color:#2c3e50;"> Tutorials and Getting Started</span> ===<br />
* [http://protegeproject.github.io/protege/getting-started/ Getting started with the Protege Desktop editor] <br />
Tutorials<br />
* [https://www.michaeldebellis.com/post/new-protege-pizza-tutorial Michael DeBellis's updated Prot&eacute;g&eacute; Pizza Tutorial]<br />
* [http://owl.cs.manchester.ac.uk/publications/talks-and-tutorials/protg-owl-tutorial/ The original Prot&eacute;g&eacute; OWL Tutorial: A step-by-step guide to modeling in OWL using the Prot&eacute;g&eacute; OWL tools]<br />
<br />
Background Information<br />
* [http://protege.stanford.edu/publications/ontology_development/ontology101.html Ontology Development 101: A Guide to creating your first ontology]<br />
* [http://www.cs.man.ac.uk/~stevensr/menupages/background.php Brief introduction to ontologies], by Robert Stevens<br />
* Semantic Web Best Practices and Deployment Working Group's [http://www.w3.org/2001/sw/BestPractices/Tutorials Semantic Web Tutorials] page<br />
* [http://arxiv.org/abs/1201.4089 A Description Logic Primer]<br />
<br />
Older documentation<br />
* [[Pr4_UG | Protege Desktop User's Guide]] - a guide on how to use Protege to create, edit, and inspect ontologies<br />
* [[Protege4Pizzas10Minutes | Pizzas in 10 minutes: A demo of modeling shortcuts]] - a quickstart guide to creating your first OWL ontology<br />
<br />
= <span style="color:#2c3e50;"> Developer Documentation </span> =<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
<br />
Please see the [https://github.com/protegeproject/webprotege WebProt&eacute;g&eacute; GitHub page]<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [[Protege5DevDocs|Prot&eacute;g&eacute; Desktop 5.x]]<br />
* [[Protege4DevDocs|Prot&eacute;g&eacute; Desktop 4.x]]<br />
* [[Protege3DevDocs|Prot&eacute;g&eacute; Desktop 3.x]]<br />
<br />
* [[ProtegeQAGuide|Guide to Quality Assurance]]<br />
<br />
<br />
= <span style="color:#2c3e50;"> Download and Support </span> =<br />
<br />
To download Prot&eacute;g&eacute; or WebProt&eacute;g&eacute; please visit our [http://protege.stanford.edu homepage]. To use the WebProt&eacute;g&eacute; server hosted at Stanford, please go to: http://webprotege.stanford.edu. <br />
<br />
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].<br />
<br />
Follow our [http://www.youtube.com/user/TheProtegeProject YouTube channel] featuring screencasts showing different features of Prot&eacute;g&eacute; and WebProt&eacute;g&eacute;.<br />
<br />
<br />
= <span style="color:#2c3e50;"> Wiki Help </span> =<br />
If you are new to using a Wiki, please see the [[Help:Contents|Help page]] page for links to User's Guides, etc. <br />
<br />
The [[Help:Contents|Help page]] also has suggestions for where to find help with using the Prot&eacute;g&eacute; application.</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Main_Page&diff=13798Main Page2022-02-17T23:14:57Z<p>Samsontu: </p>
<hr />
<div>__NOTOC__<br />
= <span style="color:#2c3e50;"> Welcome to the Prot&eacute;g&eacute; wiki! </span> =<br />
<br />
[[File:WP-classes.png|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[WebProtege|WebProt&eacute;g&eacute;]] - a powerful collaborative ontology development environment for the Web </span>]]<br />
<br />
[[File:Protege-OWL.jpg|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[Protege4UserDocs|Prot&eacute;g&eacute; Desktop]] - a fully-fledged OWL 2 ontology editor for the desktops</span>]]<br />
<br />
[https://protege.stanford.edu Prot&eacute;g&eacute;] 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. <br />
<br />
''' Quick links: [https://webprotege.stanford.edu WebProt&eacute;g&eacute; server], Prot&eacute;g&eacute; Desktop [https://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], [https://protege.stanford.edu Prot&eacute;g&eacute; website] '''<br />
<br />
= <span style="color:#2c3e50;"> User Documentation </span>=<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
* [[WebProtege|Overview]]<br />
* [[WebProtegeUsersGuide|User's Guide]]<br />
* [https://github.com/protegeproject/webprotege/wiki/WebProtégé-4.0.0-beta-x-Installation Administrator's Guide] - download and installation instructions<br />
* Use WebProt&eacute;g&eacute; now on our Stanford-hosted server: http://webprotege.stanford.edu<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [http://protegeproject.github.io/protege/ Prot&eacute;g&eacute; Desktop documentation] ([https://github.com/protegeproject/protege-distribution/releases release notes], [http://protegeproject.github.io/protege/installation/ installation instructions], [http://protege.stanford.edu/products.php#desktop-protege Protege Desktop download], [[Protege_Desktop_Old_Versions|older Protege releases download]])<br />
* [http://protegeproject.github.io/protege/views/ Views], [http://protegeproject.github.io/protege/menus/ Menus], [http://protegeproject.github.io/protege/class-expression-syntax/ Class Expression Syntax] - a short guide to some of the desktop Prot&eacute;g&eacute; interface components<br />
* [[Protege3UserDocs|Older Prot&eacute;g&eacute; releases documentation (version 3.x)]]<br />
* [[Protege-OWL_4_FAQ|Frequently Asked Questions (FAQ)]]<br />
<br />
<br />
=== <span style="color:#2c3e50;"> Tutorials and Getting Started</span> ===<br />
* [http://protegeproject.github.io/protege/getting-started/ Getting started with the Protege Desktop editor] <br />
Tutorials<br />
* [https://www.michaeldebellis.com/post/new-protege-pizza-tutorial Michael DeBellis's updatedProt&eacute;g&eacute; Pizza Tutorial]<br />
* [http://owl.cs.manchester.ac.uk/publications/talks-and-tutorials/protg-owl-tutorial/ The original Prot&eacute;g&eacute; OWL Tutorial: A step-by-step guide to modeling in OWL using the Prot&eacute;g&eacute; OWL tools]<br />
<br />
Background Information<br />
* [http://protege.stanford.edu/publications/ontology_development/ontology101.html Ontology Development 101: A Guide to creating your first ontology]<br />
* [http://www.cs.man.ac.uk/~stevensr/menupages/background.php Brief introduction to ontologies], by Robert Stevens<br />
* Semantic Web Best Practices and Deployment Working Group's [http://www.w3.org/2001/sw/BestPractices/Tutorials Semantic Web Tutorials] page<br />
* [http://arxiv.org/abs/1201.4089 A Description Logic Primer]<br />
<br />
Older documentation<br />
* [[Pr4_UG | Protege Desktop User's Guide]] - a guide on how to use Protege to create, edit, and inspect ontologies<br />
* [[Protege4Pizzas10Minutes | Pizzas in 10 minutes: A demo of modeling shortcuts]] - a quickstart guide to creating your first OWL ontology<br />
<br />
= <span style="color:#2c3e50;"> Developer Documentation </span> =<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
<br />
Please see the [https://github.com/protegeproject/webprotege WebProt&eacute;g&eacute; GitHub page]<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [[Protege5DevDocs|Prot&eacute;g&eacute; Desktop 5.x]]<br />
* [[Protege4DevDocs|Prot&eacute;g&eacute; Desktop 4.x]]<br />
* [[Protege3DevDocs|Prot&eacute;g&eacute; Desktop 3.x]]<br />
<br />
* [[ProtegeQAGuide|Guide to Quality Assurance]]<br />
<br />
<br />
= <span style="color:#2c3e50;"> Download and Support </span> =<br />
<br />
To download Prot&eacute;g&eacute; or WebProt&eacute;g&eacute; please visit our [http://protege.stanford.edu homepage]. To use the WebProt&eacute;g&eacute; server hosted at Stanford, please go to: http://webprotege.stanford.edu. <br />
<br />
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].<br />
<br />
Follow our [http://www.youtube.com/user/TheProtegeProject YouTube channel] featuring screencasts showing different features of Prot&eacute;g&eacute; and WebProt&eacute;g&eacute;.<br />
<br />
<br />
= <span style="color:#2c3e50;"> Wiki Help </span> =<br />
If you are new to using a Wiki, please see the [[Help:Contents|Help page]] page for links to User's Guides, etc. <br />
<br />
The [[Help:Contents|Help page]] also has suggestions for where to find help with using the Prot&eacute;g&eacute; application.</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Main_Page&diff=13797Main Page2022-02-17T23:13:03Z<p>Samsontu: </p>
<hr />
<div>__NOTOC__<br />
= <span style="color:#2c3e50;"> Welcome to the Prot&eacute;g&eacute; wiki! </span> =<br />
<br />
[[File:WP-classes.png|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[WebProtege|WebProt&eacute;g&eacute;]] - a powerful collaborative ontology development environment for the Web </span>]]<br />
<br />
[[File:Protege-OWL.jpg|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[Protege4UserDocs|Prot&eacute;g&eacute; Desktop]] - a fully-fledged OWL 2 ontology editor for the desktops</span>]]<br />
<br />
[https://protege.stanford.edu Prot&eacute;g&eacute;] 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. <br />
<br />
''' Quick links: [https://webprotege.stanford.edu WebProt&eacute;g&eacute; server], Prot&eacute;g&eacute; Desktop [https://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], [https://protege.stanford.edu Prot&eacute;g&eacute; website] '''<br />
<br />
= <span style="color:#2c3e50;"> User Documentation </span>=<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
* [[WebProtege|Overview]]<br />
* [[WebProtegeUsersGuide|User's Guide]]<br />
* [https://github.com/protegeproject/webprotege/wiki/WebProtégé-4.0.0-beta-x-Installation Administrator's Guide] - download and installation instructions<br />
* Use WebProt&eacute;g&eacute; now on our Stanford-hosted server: http://webprotege.stanford.edu<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [http://protegeproject.github.io/protege/ Prot&eacute;g&eacute; Desktop documentation] ([https://github.com/protegeproject/protege-distribution/releases release notes], [http://protegeproject.github.io/protege/installation/ installation instructions], [http://protege.stanford.edu/products.php#desktop-protege Protege Desktop download], [[Protege_Desktop_Old_Versions|older Protege releases download]])<br />
* [http://protegeproject.github.io/protege/views/ Views], [http://protegeproject.github.io/protege/menus/ Menus], [http://protegeproject.github.io/protege/class-expression-syntax/ Class Expression Syntax] - a short guide to some of the desktop Prot&eacute;g&eacute; interface components<br />
* [[Protege3UserDocs|Older Prot&eacute;g&eacute; releases documentation (version 3.x)]]<br />
* [[Protege-OWL_4_FAQ|Frequently Asked Questions (FAQ)]]<br />
<br />
<br />
=== <span style="color:#2c3e50;"> Tutorials and Getting Started</span> ===<br />
* [http://protegeproject.github.io/protege/getting-started/ Getting started with the Protege Desktop editor] <br />
** Tutorials<br />
* [https://www.michaeldebellis.com/post/new-protege-pizza-tutorial Michael DeBellis's updatedProt&eacute;g&eacute; Pizza Tutorial]<br />
* [http://owl.cs.manchester.ac.uk/publications/talks-and-tutorials/protg-owl-tutorial/ The original Prot&eacute;g&eacute; OWL Tutorial: A step-by-step guide to modeling in OWL using the Prot&eacute;g&eacute; OWL tools]<br />
<br />
** Background Information<br />
* [http://protege.stanford.edu/publications/ontology_development/ontology101.html Ontology Development 101: A Guide to creating your first ontology]<br />
* [http://www.cs.man.ac.uk/~stevensr/menupages/background.php Brief introduction to ontologies], by Robert Stevens<br />
* Semantic Web Best Practices and Deployment Working Group's [http://www.w3.org/2001/sw/BestPractices/Tutorials Semantic Web Tutorials] page<br />
* [http://arxiv.org/abs/1201.4089 A Description Logic Primer]<br />
<br />
** Older documentation<br />
* [[Pr4_UG | Protege Desktop User's Guide]] - a guide on how to use Protege to create, edit, and inspect ontologies<br />
* [[Protege4Pizzas10Minutes | Pizzas in 10 minutes: A demo of modeling shortcuts]] - a quickstart guide to creating your first OWL ontology<br />
<br />
= <span style="color:#2c3e50;"> Developer Documentation </span> =<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
<br />
Please see the [https://github.com/protegeproject/webprotege WebProt&eacute;g&eacute; GitHub page]<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [[Protege5DevDocs|Prot&eacute;g&eacute; Desktop 5.x]]<br />
* [[Protege4DevDocs|Prot&eacute;g&eacute; Desktop 4.x]]<br />
* [[Protege3DevDocs|Prot&eacute;g&eacute; Desktop 3.x]]<br />
<br />
* [[ProtegeQAGuide|Guide to Quality Assurance]]<br />
<br />
<br />
= <span style="color:#2c3e50;"> Download and Support </span> =<br />
<br />
To download Prot&eacute;g&eacute; or WebProt&eacute;g&eacute; please visit our [http://protege.stanford.edu homepage]. To use the WebProt&eacute;g&eacute; server hosted at Stanford, please go to: http://webprotege.stanford.edu. <br />
<br />
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].<br />
<br />
Follow our [http://www.youtube.com/user/TheProtegeProject YouTube channel] featuring screencasts showing different features of Prot&eacute;g&eacute; and WebProt&eacute;g&eacute;.<br />
<br />
<br />
= <span style="color:#2c3e50;"> Wiki Help </span> =<br />
If you are new to using a Wiki, please see the [[Help:Contents|Help page]] page for links to User's Guides, etc. <br />
<br />
The [[Help:Contents|Help page]] also has suggestions for where to find help with using the Prot&eacute;g&eacute; application.</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Main_Page&diff=13796Main Page2022-02-17T23:09:49Z<p>Samsontu: </p>
<hr />
<div>__NOTOC__<br />
= <span style="color:#2c3e50;"> Welcome to the Prot&eacute;g&eacute; wiki! </span> =<br />
<br />
[[File:WP-classes.png|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[WebProtege|WebProt&eacute;g&eacute;]] - a powerful collaborative ontology development environment for the Web </span>]]<br />
<br />
[[File:Protege-OWL.jpg|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[Protege4UserDocs|Prot&eacute;g&eacute; Desktop]] - a fully-fledged OWL 2 ontology editor for the desktops</span>]]<br />
<br />
[https://protege.stanford.edu Prot&eacute;g&eacute;] 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. <br />
<br />
''' Quick links: [https://webprotege.stanford.edu WebProt&eacute;g&eacute; server], Prot&eacute;g&eacute; Desktop [https://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], [https://protege.stanford.edu Prot&eacute;g&eacute; website] '''<br />
<br />
= <span style="color:#2c3e50;"> User Documentation </span>=<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
* [[WebProtege|Overview]]<br />
* [[WebProtegeUsersGuide|User's Guide]]<br />
* [https://github.com/protegeproject/webprotege/wiki/WebProtégé-4.0.0-beta-x-Installation Administrator's Guide] - download and installation instructions<br />
* Use WebProt&eacute;g&eacute; now on our Stanford-hosted server: http://webprotege.stanford.edu<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [http://protegeproject.github.io/protege/ Prot&eacute;g&eacute; Desktop documentation] ([https://github.com/protegeproject/protege-distribution/releases release notes], [http://protegeproject.github.io/protege/installation/ installation instructions], [http://protege.stanford.edu/products.php#desktop-protege Protege Desktop download], [[Protege_Desktop_Old_Versions|older Protege releases download]])<br />
* [[Protege3UserDocs|Older Prot&eacute;g&eacute; releases documentation (version 3.x)]]<br />
* [[Protege-OWL_4_FAQ|Frequently Asked Questions (FAQ)]]<br />
<br />
<br />
=== <span style="color:#2c3e50;"> Tutorials and Getting Started</span> ===<br />
* [http://protegeproject.github.io/protege/getting-started/ Getting started with the Protege Desktop editor] <br />
* [http://protegeproject.github.io/protege/views/ Views], [http://protegeproject.github.io/protege/menus/ Menus], [http://protegeproject.github.io/protege/class-expression-syntax/ Class Expression Syntax] - a short guide to some of the interface components<br />
* [https://www.michaeldebellis.com/post/new-protege-pizza-tutorial Michael DeBellis's updatedProt&eacute;g&eacute; Pizza Tutorial]<br />
* [http://owl.cs.manchester.ac.uk/publications/talks-and-tutorials/protg-owl-tutorial/ The original Prot&eacute;g&eacute; OWL Tutorial: A step-by-step guide to modeling in OWL using the Prot&eacute;g&eacute; OWL tools]<br />
<br />
** Background Information<br />
* [http://protege.stanford.edu/publications/ontology_development/ontology101.html Ontology Development 101: A Guide to creating your first ontology]<br />
* [http://www.cs.man.ac.uk/~stevensr/menupages/background.php Brief introduction to ontologies], by Robert Stevens<br />
* Semantic Web Best Practices and Deployment Working Group's [http://www.w3.org/2001/sw/BestPractices/Tutorials Semantic Web Tutorials] page<br />
* [http://arxiv.org/abs/1201.4089 A Description Logic Primer]<br />
<br />
** Older documentation<br />
* [[Pr4_UG | Protege Desktop User's Guide]] - a guide on how to use Protege to create, edit, and inspect ontologies<br />
* [[Protege4Pizzas10Minutes | Pizzas in 10 minutes: A demo of modeling shortcuts]] - a quickstart guide to creating your first OWL ontology<br />
<br />
= <span style="color:#2c3e50;"> Developer Documentation </span> =<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
<br />
Please see the [https://github.com/protegeproject/webprotege WebProt&eacute;g&eacute; GitHub page]<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [[Protege5DevDocs|Prot&eacute;g&eacute; Desktop 5.x]]<br />
* [[Protege4DevDocs|Prot&eacute;g&eacute; Desktop 4.x]]<br />
* [[Protege3DevDocs|Prot&eacute;g&eacute; Desktop 3.x]]<br />
<br />
* [[ProtegeQAGuide|Guide to Quality Assurance]]<br />
<br />
<br />
= <span style="color:#2c3e50;"> Download and Support </span> =<br />
<br />
To download Prot&eacute;g&eacute; or WebProt&eacute;g&eacute; please visit our [http://protege.stanford.edu homepage]. To use the WebProt&eacute;g&eacute; server hosted at Stanford, please go to: http://webprotege.stanford.edu. <br />
<br />
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].<br />
<br />
Follow our [http://www.youtube.com/user/TheProtegeProject YouTube channel] featuring screencasts showing different features of Prot&eacute;g&eacute; and WebProt&eacute;g&eacute;.<br />
<br />
<br />
= <span style="color:#2c3e50;"> Wiki Help </span> =<br />
If you are new to using a Wiki, please see the [[Help:Contents|Help page]] page for links to User's Guides, etc. <br />
<br />
The [[Help:Contents|Help page]] also has suggestions for where to find help with using the Prot&eacute;g&eacute; application.</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Main_Page&diff=13795Main Page2022-02-17T23:03:57Z<p>Samsontu: </p>
<hr />
<div>__NOTOC__<br />
= <span style="color:#2c3e50;"> Welcome to the Prot&eacute;g&eacute; wiki! </span> =<br />
<br />
[[File:WP-classes.png|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[WebProtege|WebProt&eacute;g&eacute;]] - a powerful collaborative ontology development environment for the Web </span>]]<br />
<br />
[[File:Protege-OWL.jpg|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[Protege4UserDocs|Prot&eacute;g&eacute; Desktop]] - a fully-fledged OWL 2 ontology editor for the desktops</span>]]<br />
<br />
[https://protege.stanford.edu Prot&eacute;g&eacute;] 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. <br />
<br />
''' Quick links: [https://webprotege.stanford.edu WebProt&eacute;g&eacute; server], Prot&eacute;g&eacute; Desktop [https://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], [https://protege.stanford.edu Prot&eacute;g&eacute; website] '''<br />
<br />
= <span style="color:#2c3e50;"> User Documentation </span>=<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
* [[WebProtege|Overview]]<br />
* [[WebProtegeUsersGuide|User's Guide]]<br />
* [https://github.com/protegeproject/webprotege/wiki/WebProtégé-4.0.0-beta-x-Installation Administrator's Guide] - download and installation instructions<br />
* Use WebProt&eacute;g&eacute; now on our Stanford-hosted server: http://webprotege.stanford.edu<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [http://protegeproject.github.io/protege/ Prot&eacute;g&eacute; Desktop documentation] ([https://github.com/protegeproject/protege-distribution/releases release notes], [http://protegeproject.github.io/protege/installation/ installation instructions], [http://protege.stanford.edu/products.php#desktop-protege Protege Desktop download], [[Protege_Desktop_Old_Versions|older Protege releases download]])<br />
* [[Protege3UserDocs|Older Prot&eacute;g&eacute; releases documentation (version 3.x)]]<br />
* [[Protege-OWL_4_FAQ|Frequently Asked Questions (FAQ)]]<br />
<br />
<br />
=== <span style="color:#2c3e50;"> Tutorials and Getting Started</span> ===<br />
* [http://protegeproject.github.io/protege/getting-started/ Getting started with the Protege Desktop editor] - a short guide to the interface<br />
* [https://www.michaeldebellis.com/post/new-protege-pizza-tutorial Michael DeBellis's updatedProt&eacute;g&eacute; Pizza Tutorial]<br />
* [http://owl.cs.manchester.ac.uk/publications/talks-and-tutorials/protg-owl-tutorial/ The original Prot&eacute;g&eacute; OWL Tutorial: A step-by-step guide to modeling in OWL using the Prot&eacute;g&eacute; OWL tools]<br />
<br />
** Background Information **<br />
* [http://protege.stanford.edu/publications/ontology_development/ontology101.html Ontology Development 101: A Guide to creating your first ontology]<br />
* [http://www.cs.man.ac.uk/~stevensr/menupages/background.php Brief introduction to ontologies], by Robert Stevens<br />
* Semantic Web Best Practices and Deployment Working Group's [http://www.w3.org/2001/sw/BestPractices/Tutorials Semantic Web Tutorials] page<br />
* [http://arxiv.org/abs/1201.4089 A Description Logic Primer]<br />
<br />
** Older documentation<br />
* [[Pr4_UG | Protege Desktop User's Guide]] - a guide on how to use Protege to create, edit, and inspect ontologies<br />
* [[Protege4Pizzas10Minutes | Pizzas in 10 minutes: A demo of modeling shortcuts]] - a quickstart guide to creating your first OWL ontology<br />
<br />
= <span style="color:#2c3e50;"> Developer Documentation </span> =<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
<br />
Please see the [https://github.com/protegeproject/webprotege WebProt&eacute;g&eacute; GitHub page]<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [[Protege5DevDocs|Prot&eacute;g&eacute; Desktop 5.x]]<br />
* [[Protege4DevDocs|Prot&eacute;g&eacute; Desktop 4.x]]<br />
* [[Protege3DevDocs|Prot&eacute;g&eacute; Desktop 3.x]]<br />
<br />
* [[ProtegeQAGuide|Guide to Quality Assurance]]<br />
<br />
<br />
= <span style="color:#2c3e50;"> Download and Support </span> =<br />
<br />
To download Prot&eacute;g&eacute; or WebProt&eacute;g&eacute; please visit our [http://protege.stanford.edu homepage]. To use the WebProt&eacute;g&eacute; server hosted at Stanford, please go to: http://webprotege.stanford.edu. <br />
<br />
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].<br />
<br />
Follow our [http://www.youtube.com/user/TheProtegeProject YouTube channel] featuring screencasts showing different features of Prot&eacute;g&eacute; and WebProt&eacute;g&eacute;.<br />
<br />
<br />
= <span style="color:#2c3e50;"> Wiki Help </span> =<br />
If you are new to using a Wiki, please see the [[Help:Contents|Help page]] page for links to User's Guides, etc. <br />
<br />
The [[Help:Contents|Help page]] also has suggestions for where to find help with using the Prot&eacute;g&eacute; application.</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Main_Page&diff=13794Main Page2022-02-17T23:00:34Z<p>Samsontu: </p>
<hr />
<div>__NOTOC__<br />
= <span style="color:#2c3e50;"> Welcome to the Prot&eacute;g&eacute; wiki! </span> =<br />
<br />
[[File:WP-classes.png|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[WebProtege|WebProt&eacute;g&eacute;]] - a powerful collaborative ontology development environment for the Web </span>]]<br />
<br />
[[File:Protege-OWL.jpg|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[Protege4UserDocs|Prot&eacute;g&eacute; Desktop]] - a fully-fledged OWL 2 ontology editor for the desktops</span>]]<br />
<br />
[https://protege.stanford.edu Prot&eacute;g&eacute;] 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. <br />
<br />
''' Quick links: [https://webprotege.stanford.edu WebProt&eacute;g&eacute; server], Prot&eacute;g&eacute; Desktop [https://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], [https://protege.stanford.edu Prot&eacute;g&eacute; website] '''<br />
<br />
= <span style="color:#2c3e50;"> User Documentation </span>=<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
* [[WebProtege|Overview]]<br />
* [[WebProtegeUsersGuide|User's Guide]]<br />
* [https://github.com/protegeproject/webprotege/wiki/WebProtégé-4.0.0-beta-x-Installation Administrator's Guide] - download and installation instructions<br />
* Use WebProt&eacute;g&eacute; now on our Stanford-hosted server: http://webprotege.stanford.edu<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [http://protegeproject.github.io/protege/ Prot&eacute;g&eacute; Desktop documentation] ([https://github.com/protegeproject/protege-distribution/releases release notes], [http://protegeproject.github.io/protege/installation/ installation instructions], [http://protege.stanford.edu/products.php#desktop-protege Protege Desktop download], [[Protege_Desktop_Old_Versions|older Protege releases download]])<br />
* [[Protege3UserDocs|Older Prot&eacute;g&eacute; releases documentation (version 3.x)]]<br />
* [[Protege-OWL_4_FAQ|Frequently Asked Questions (FAQ)]]<br />
<br />
<br />
=== <span style="color:#2c3e50;"> Tutorials and Getting Started</span> ===<br />
* [http://protegeproject.github.io/protege/getting-started/ Getting started with the Protege Desktop editor] - a short guide to the interface<br />
<br />
<br />
* [http://protege.stanford.edu/publications/ontology_development/ontology101.html Ontology Development 101: A Guide to creating your first ontology]<br />
* [http://www.cs.man.ac.uk/~stevensr/menupages/background.php Brief introduction to ontologies], by Robert Stevens<br />
<br />
* [https://www.michaeldebellis.com/post/new-protege-pizza-tutorial Michael DeBellis's updatedProt&eacute;g&eacute; Pizza Tutorial]<br />
* [http://owl.cs.manchester.ac.uk/publications/talks-and-tutorials/protg-owl-tutorial/ The original Prot&eacute;g&eacute; OWL Tutorial: A step-by-step guide to modeling in OWL using the Prot&eacute;g&eacute; OWL tools]<br />
* Semantic Web Best Practices and Deployment Working Group's [http://www.w3.org/2001/sw/BestPractices/Tutorials Semantic Web Tutorials] page<br />
* [[Pr4_UG | Protege Desktop User's Guide]] - a guide on how to use Protege to create, edit, and inspect ontologies<br />
* [[Protege4Pizzas10Minutes | Pizzas in 10 minutes: A demo of modeling shortcuts]] - a quickstart guide to creating your first OWL ontology<br />
* [http://arxiv.org/abs/1201.4089 A Description Logic Primer]<br />
<br />
<br />
<br />
= <span style="color:#2c3e50;"> Developer Documentation </span> =<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
<br />
Please see the [https://github.com/protegeproject/webprotege WebProt&eacute;g&eacute; GitHub page]<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [[Protege5DevDocs|Prot&eacute;g&eacute; Desktop 5.x]]<br />
* [[Protege4DevDocs|Prot&eacute;g&eacute; Desktop 4.x]]<br />
* [[Protege3DevDocs|Prot&eacute;g&eacute; Desktop 3.x]]<br />
<br />
* [[ProtegeQAGuide|Guide to Quality Assurance]]<br />
<br />
<br />
= <span style="color:#2c3e50;"> Download and Support </span> =<br />
<br />
To download Prot&eacute;g&eacute; or WebProt&eacute;g&eacute; please visit our [http://protege.stanford.edu homepage]. To use the WebProt&eacute;g&eacute; server hosted at Stanford, please go to: http://webprotege.stanford.edu. <br />
<br />
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].<br />
<br />
Follow our [http://www.youtube.com/user/TheProtegeProject YouTube channel] featuring screencasts showing different features of Prot&eacute;g&eacute; and WebProt&eacute;g&eacute;.<br />
<br />
<br />
= <span style="color:#2c3e50;"> Wiki Help </span> =<br />
If you are new to using a Wiki, please see the [[Help:Contents|Help page]] page for links to User's Guides, etc. <br />
<br />
The [[Help:Contents|Help page]] also has suggestions for where to find help with using the Prot&eacute;g&eacute; application.</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Main_Page&diff=13785Main Page2022-02-16T07:11:07Z<p>Samsontu: </p>
<hr />
<div>__NOTOC__<br />
= <span style="color:#2c3e50;"> Welcome to the Prot&eacute;g&eacute; wiki! </span> =<br />
<br />
[[File:WP-classes.png|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[WebProtege|WebProt&eacute;g&eacute;]] - a powerful collaborative ontology development environment for the Web </span>]]<br />
<br />
[[File:Protege-OWL.jpg|right|300px|thumb|<span style="color:#2c3e50; font-weight:bold;">[[Protege4UserDocs|Prot&eacute;g&eacute; Desktop]] - a fully-fledged OWL 2 ontology editor for the desktops</span>]]<br />
<br />
[http://protege.stanford.edu Prot&eacute;g&eacute;] 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. <br />
<br />
''' Quick links: [http://webprotege.stanford.edu WebProt&eacute;g&eacute; server], Prot&eacute;g&eacute; 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 Prot&eacute;g&eacute; website] '''<br />
<br />
<br />
= <span style="color:#2c3e50;"> User Documentation </span>=<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
* [[WebProtege|Overview]]<br />
* [[WebProtegeUsersGuide|User's Guide]]<br />
* [https://github.com/protegeproject/webprotege/wiki/WebProtégé-4.0.0-beta-x-Installation Administrator's Guide] - download and installation instructions<br />
* Use WebProt&eacute;g&eacute; now on our Stanford-hosted server: http://webprotege.stanford.edu<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [http://protegeproject.github.io/protege/ Prot&eacute;g&eacute; Desktop documentation] ([https://github.com/protegeproject/protege-distribution/releases release notes], [http://protegeproject.github.io/protege/installation/ installation instructions], [http://protege.stanford.edu/products.php#desktop-protege Protege Desktop download], [[Protege_Desktop_Old_Versions|older Protege releases download]])<br />
* [[Protege3UserDocs|Older Prot&eacute;g&eacute; releases documentation (version 3.x)]]<br />
* [[Protege-OWL_4_FAQ|Frequently Asked Questions (FAQ)]]<br />
<br />
<br />
=== <span style="color:#2c3e50;"> Tutorials and Getting Started</span> ===<br />
* [http://protege.stanford.edu/publications/ontology_development/ontology101.html Ontology Development 101: A Guide to creating your first ontology]<br />
* [http://www.cs.man.ac.uk/~stevensr/menupages/background.php Brief introduction to ontologies], by Robert Stevens<br />
* [http://owl.cs.manchester.ac.uk/publications/talks-and-tutorials/protg-owl-tutorial/ Prot&eacute;g&eacute; OWL Tutorial: A step-by-step guide to modeling in OWL using the Prot&eacute;g&eacute; OWL tools]<br />
* Semantic Web Best Practices and Deployment Working Group's [http://www.w3.org/2001/sw/BestPractices/Tutorials Semantic Web Tutorials] page<br />
* [[Protege4GettingStarted | Getting started with the Protege Desktop editor]] - a short guide to the interface<br />
* [[Pr4_UG | Protege Desktop User's Guide]] - a guide on how to use Protege to create, edit, and inspect ontologies<br />
* [[Protege4Pizzas10Minutes | Pizzas in 10 minutes: A demo of modeling shortcuts]] - a quickstart guide to creating your first OWL ontology<br />
* 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).<br />
* [http://arxiv.org/abs/1201.4089 A Description Logic Primer]<br />
<br />
<br />
<br />
= <span style="color:#2c3e50;"> Developer Documentation </span> =<br />
<br />
=== <span style="color:#2c3e50;"> WebProt&eacute;g&eacute; </span> ===<br />
<br />
Please see the [https://github.com/protegeproject/webprotege WebProt&eacute;g&eacute; GitHub page]<br />
<br />
=== <span style="color:#2c3e50;"> Prot&eacute;g&eacute; Desktop </span> ===<br />
* [[Protege5DevDocs|Prot&eacute;g&eacute; Desktop 5.x]]<br />
* [[Protege4DevDocs|Prot&eacute;g&eacute; Desktop 4.x]]<br />
* [[Protege3DevDocs|Prot&eacute;g&eacute; Desktop 3.x]]<br />
<br />
* [[ProtegeQAGuide|Guide to Quality Assurance]]<br />
<br />
<br />
= <span style="color:#2c3e50;"> Download and Support </span> =<br />
<br />
To download Prot&eacute;g&eacute; or WebProt&eacute;g&eacute; please visit our [http://protege.stanford.edu homepage]. To use the WebProt&eacute;g&eacute; server hosted at Stanford, please go to: http://webprotege.stanford.edu. <br />
<br />
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].<br />
<br />
Follow our [http://www.youtube.com/user/TheProtegeProject YouTube channel] featuring screencasts showing different features of Prot&eacute;g&eacute; and WebProt&eacute;g&eacute;.<br />
<br />
<br />
= <span style="color:#2c3e50;"> Wiki Help </span> =<br />
If you are new to using a Wiki, please see the [[Help:Contents|Help page]] page for links to User's Guides, etc. <br />
<br />
The [[Help:Contents|Help page]] also has suggestions for where to find help with using the Prot&eacute;g&eacute; application.</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Help:Contents&diff=13784Help:Contents2022-02-14T19:34:01Z<p>Samsontu: /* Administrators */</p>
<hr />
<div>__TOC__<br />
<br />
<br />
== Wiki Help ==<br />
<br />
=== Users ===<br />
* Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using MediaWiki software.<br />
* [http://www.mediawiki.org/wiki/Help:FAQ MediaWiki FAQ]<br />
* Browse the [http://semantic-mediawiki.org/index.php/Help:Semantics Semantic MediaWiki user manual] to learn more about the semantic underpinnings of this Wiki.<br />
* Learn how to do [http://semantic-mediawiki.org/wiki/Help:Semantic_search semantic searches] on this wiki.<br />
<br />
=== Administrators ===<br />
* [ontoworld.org/wiki/Semantic_MediaWiki Semantic MediaWiki] extension installed<br />
* [http://www.mediawiki.org/wiki/Help:Configuration_settings Configuration settings list]<br />
* [http://www.mediawiki.org/wiki/Extension:Semantic_Forms Semantic Forms] extension installed<br />
<br />
== Protege Help ==<br />
If you are looking for help on how to use Protege, a good place to start is the [http://protege.stanford.edu/support.php#documentationSupport documentation section] of the Protege website. We also have a number of mailing lists to which you can subscribe and post questions. More information about mailing lists and list archives is available on the [http://protege.stanford.edu/support.php#mailingListSupport support page] of the Protege website.</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=WebProtegeReleaseNotes&diff=13783WebProtegeReleaseNotes2022-02-14T19:31:26Z<p>Samsontu: </p>
<hr />
<div><span style="padding:0; margin:0; font-size:1.9em; font-weight:bold; word-spacing:-2px;">WebProtege Release Notes</span><br /><br />
<br />
<div style="background: #FFCCCC; border: 1px solid #AE5B08; padding: 5px 5px 5px 5px; margin: 15px 430px 15px 0; "><br />
<span style="font-weight:bold;"> We have migrated all WebProtege releases and release notes following build 105 to [https://github.com/protegeproject/webprotege/releases GitHub]. For all new releases, please use the [https://github.com/protegeproject/webprotege/releases WebProtege GitHub page] to access the release notes.</span><br />
</div><br />
<br />
<br />
__TOC__<br />
<br />
'''Go back to the [[WebProtege|WebProtege main page]].<br />
<br />
== WebProtege Build 105 (July 24, 2013) ==<br />
<br />
[[File:WP_UsagePortlet.png|thumb|400px|right]]<br />
<br />
'''New portlets:'''<br />
<br />
* '''Usage''' portlet - shows the usage for the selected class, property or individual. Usage can be filtered by type of entity, axiom etc. and can be sorted by entity, entity type, axiom type etc.<br />
* '''Ontology Id''' portlet - displays the id of the project root ontology (currently read only)<br />
* '''Ontology Annotations''' - displays the annotations for the project root ontology<br />
<br />
'''Bug Fixes:'''<br />
<br />
* Some application properties were ignored e.g. ''Application Name'' -- Fixed<br />
* Several fixes of the [[PropertyFormPortlet|Property Form Portlet]]:<br />
** The [[PropertyFormPortlet#Using_grids_.28tables.29|Property Grid]] widget didn't work at all -- Fixed<br />
** Simple property widgets would display strange values after editing -- Fixed<br />
* Changed the size of portlets in the default layout (people with local installations who want these changes will need to delete the existing default configuration files so that the new ones are copied over on start up).<br />
<br />
'''Enhancements:'''<br />
<br />
* Some cosmetic UI enhancements e.g. progress bars and message boxes now use native gwt widgets<br />
<br />
<br />
== WebProtege Build 104 (July 5, 2013) ==<br />
<br />
'''User Interface:'''<br />
* Fixed a design issue with the properties portlet which caused annotations not to be displayed.<br />
* Made the properties porlet display superclasses that are SomeValuesFrom and HasValue restrictions as property values.<br />
<br />
'''OBO:'''<br />
* WebProtege now uses the "reference" OBO Format parser for parsing OBO ontologies.<br />
* Improved the layout and utility of the various OBO metadata editing widgets.<br />
<br />
'''Other:'''<br />
* Fixed a bug that caused the link in watch notification emails to be incorrect.<br />
* Turned off recaptcha verification from sign up dialog.<br />
<br />
<br />
<br />
== WebProtege Build 103 (May 20, 2013) ==<br />
<br />
* Fixed a problem that caused the class hierarchy stop expanding in some cases<br />
* Changed the presentation of notes so that note status (resolved or unresolved) is shown on a new line<br />
<br />
<br />
== WebProtege Build 102 (May 15, 2013) ==<br />
<br />
* 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.<br />
<br />
* Fixed problem related to watches not being persisted in some cases<br />
<br />
<br />
== WebProtege Build 101 (May 2, 2013) ==<br />
<br />
* Fixed problem related to downloading of ontologies from Firefox<br />
<br />
<br />
== MAJOR NEW WebProtege Release (Build 100, April 25, 2013) ==<br />
<br />
[[File:WP-classes.png|thumb|400px|right]]<br />
<br />
We are pleased to announce the availability of a new version of WebProtege at http://webprotege.stanford.edu. <br />
This release constitutes a major new release with many new features and improvements.<br />
<br />
'''Please, try it out and let us know what you think!'''<br />
<br />
<br />
Read below about some of the more exciting features:<br />
<br />
<br />
'''Sharing:'''<br />
<br />
* '''"Google docs" style mode of operation''' - upload and share ontologies with colleagues and collaborators.<br />
* '''Access control''' - ontologies can be public or private with controlled lists of users who can read, write and comment.<br />
* '''Discussion support''' - discussion threads for entities make it easy to add issues, todo notes and queries.<br />
<br />
<br />
'''User Interface:'''<br />
<br />
* '''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)<br />
* '''Editing assistance''' - autocompletion for class, property and individual names<br />
* '''Fast editing''' - on-the-fly creation of properties, classes and individuals (you not longer need to define classes and properties upfront before using them)<br />
* '''Bulk creation''' - quickly sketch out class and property hierarchies using bulk entry for subclasses and subproperties<br />
* '''OBO support''' - import OBO ontologies and use forms designed for editing OBO constructs and metadata <br />
<br />
<br />
'''OWL 2 support:'''<br />
<br />
This release uses the [http://owlapi.sourceforge.net/ OWL API] and supports editing of lightweight OWL 2 ontologies natively.<br />
<br />
<br />
'''Change Tracking:'''<br />
<br />
* '''Full change-history logging''' - inspect changes by change type, timestamp, author etc.<br />
* '''Revision tracking''' - download any revision of an ontology at any time. <br />
<br />
<br />
'''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]]'''.<br />
<br />
<br />
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.<br />
<br />
== WebProtege 1.0 Final Release (April 25, 2013) ==<br />
<br />
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.<br />
<br />
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.<br />
<br />
There are a few important announcements related to the WebProtege 1.0 release:<br />
<br />
* The WebProtege 1.0 demo server has been moved from http://webprotege.stanford.edu to http://wp-obs.stanford.edu<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
''' Enhancements and Fixes in WebProtege 1.0 '''<br />
<br />
* 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.<br />
<br />
* 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).<br />
<br />
* The AllPropertiesPortlet also includes now the rdfs:seeAlso and rdfs:isDefinedBy in the list of properties that can be edited for an entity.<br />
<br />
* 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.<br />
<br />
* Double-clicking on a row in the Changes portlet will bring up a new window with the details on the change.<br />
<br />
<br />
''' Download and Install '''<br />
<br />
The download and install instructions are available in the [[WebProtege1.0AdminGuide|WebProtege 1.0 Administrator's Guide]].<br />
<br />
== WebProtege Beta Series ==<br />
<br />
=== February 7, 2013 ===<br />
<br />
'''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.'''<br />
<br />
<br />
'''We are very excited to announce WebProtege 2.0 Beta!'''<br />
<br />
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.<br />
<br />
Key new features:<br />
<br />
* 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.<br />
<br />
* 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.<br />
<br />
* 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).<br />
<br />
[[Image:WebProtege_2.0_Beta.png]]<br />
<br />
<br />
=== January 12, 2013 ===<br />
<br />
[[Image:WebProtege_2.0_Beta.png|thumb|400px|right|Screenshot of OBO-specific widgets - new in 2.0 beta!]]<br />
<br />
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:<br /><br /><br />
<br />
'''[http://webprotege-beta.stanford.edu/ http://webprotege-beta.stanford.edu/]'''<br /><br /><br />
<br />
''' Release Highlights '''<br />
<br />
''This section describes changes relative to WebProtege 0.5''<br />
<br />
<ul><br />
<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><br />
<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><br />
<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><br />
</ul><br />
<br />
=== June 4, 2012 ===<br />
<br />
<ul><br />
<li>Initial software release to demo server [http://webprotege-beta.stanford.edu/ http://webprotege-beta.stanford.edu/].</li><br />
</ul><br />
<br />
== WebProtege 0.5 Beta Series ==<br />
<br />
=== Beta Build 501 - May 28, 2011 ===<br />
<br />
* The ''All Properties Portlet'' (used to show the annotation properties and other properties attached to entities) supports now the '''editing of instance values'''. <br />
<br />
* Fixes for the editing of String values in the ''All Properties Portlet''<br />
<br />
* 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.<br />
<br />
<br />
=== Beta Build 500 - May 13, 2011 ===<br />
<br />
* 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<br />
<br />
<br />
==== New functionality ====<br />
<br />
* '''Restriction editing''' is supported in the ''Restriction Portlet''. The portlet has support for auto-complete for entity names.<br />
<br />
* '''Threaded notes and discussions''' are now supported in the ''Notes Tree Portlet''.<br />
<br />
* 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.<br />
<br />
* 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.<br />
<br />
* WebProtege now '''enforces the read and write access right permissions''' as defined in the [[Protege_Client_Server_Tutorial_Configuration|metaproject]].<br />
<br />
* 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.<br />
<br />
* 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.<br />
<br />
* 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.<br />
<br />
* 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.<br />
<br />
* 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.<br />
<br />
* Users with adequate access rights can '''create new users''' from the Options menu -> Add new user.<br />
<br />
* 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.<br />
<br />
<br />
==== UI Layout Enhancements ====<br />
<br />
* 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).<br />
<br />
* 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]].<br />
<br />
* '''New property form widgets''':<br />
** Instance check box<br />
** Instance radio button<br />
** Instance combo-box<br />
** Class select widget<br />
** Property select widget<br />
<br />
* 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.<br />
<br />
* 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.<br />
<br />
* 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).<br />
<br />
* 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.<br />
<br />
* 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.<br />
<br />
* 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.<br />
<br />
* You may '''save the layout''' from the Ontology toolbar using the Save icon (right-most icon). This feature is still under development.<br />
<br />
* It is now possible to set the order of a portlet in a tab in the configuration xml by using the <index> element.<br />
<br />
<br />
==== Other enhancements and bug fixes ====<br />
<br />
* Better support for '''linking terms from [http://bioportal.bioontology.org BioPortal] ontologies''' with the BioPortal Reference Portlet:<br />
** Added support for composite search: each search term will be expanded<br />
** Added support for searching on synonyms and on other property values<br />
** 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. <br />
** The search can be restricted to a subset of BioPortal ontologies<br />
<br />
* The '''Parents Portlet''' displays the direct superclasses of the selected class with clickable links for easy navigation.<br />
<br />
* 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.<br />
<br />
* Fixed a resizing issue for the top panel of WebProtege.<br />
<br />
* 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.<br />
<br />
* Various other bug fixes and enhancements<br />
<br />
* Updated [[WebProtegeDevelopersGuide|developer documentation]] on setting up WebProtege in Eclipse.<br />
<br />
<br />
== WebProtege 0.5 Alpha Series ==<br />
<br />
=== Build 300 - May 12, 2010 ===<br />
<br />
* Various fixes and enhancements<br />
<br />
=== Build 200 - August 15, 2009 ===<br />
<br />
==== Critical Changes (please read) ====<br />
<br />
<ul><br />
<li>Upgraded to [http://code.google.com/webtoolkit/releases/release-notes-1.7.0.html#Release_Notes_Current GWT 1.7].</li><br />
<br />
<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.<br />
<br />
<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:<br />
<pre><br />
# Defaults to false; change to true to run WebProtege in external server mode<br />
load.ontologies.from.protege.server=true<br />
<br />
# Use to specify an alternative location for the metaproject if running in local mode<br />
local.metaproject.path=/tmp/metaproject.pprj<br />
<br />
# Hostname of the Protege server if WebProtege is running in external server mode; can also contain a port number<br />
server.hostname=localhost<br />
<br />
# Username that WebProtege uses to connect to the Protege server if running in external server mode<br />
webprotege.user=webprotege<br />
<br />
# Password that WebProtege uses to connect to the Protege server if running in external server mode<br />
webprotege.password=webprotege<br />
<br />
# Automatic save interval for ontologies if running in local mode (we recommend the database back-end instead of file mode)<br />
server.save.interval.sec=120<br />
</pre><br />
<br />
Values of properties listed above should be changed to match your custom WebProtege installation.<br />
</li><br />
<br />
<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><br />
<br />
<li style="padding-top:5px;">Users can now open multiple ontologies in WebProtege. Each ontology is displayed in a separate tab.</li><br />
</ul><br />
<br />
==== Other Changes ====<br />
<br />
<ul><br />
<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><br />
<br />
<li style="padding-top:5px;">Added more support for editing; users with write permission on a particular project are now able to:<br />
<ul><br />
<li>Create and delete classes in the Classes tab</li><br />
<li>Create and delete properties in the Properties tab</li><br />
<li>Edit string property values in the Properties portlet</li><br />
<li>Edit the domain and range of properties in the Properties tab</li><br />
</ul><br />
</li><br />
<br />
<li style="padding-top:5px;">New portlet is available; the BioPortal Search portlet allows users to search for terms in the bioontology.org/tools/portal/bioportal.html BioPortal repository and import the terms as references in WebProtege ontologies.</li><br />
<br />
<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:<br /><br /><br />
<ul><br />
<li>textfield</li><br />
<li>textarea</li><br />
<li>HTML pane</li><br />
<li>instance grid (similar to the InstanceTable in Protege standalone)</li><br />
<li>external reference</li><br />
<li>multifield</li><br />
<li>combo-box; not working yet... :)</li>.<br />
</ul><br />
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><br />
<br />
<li style="padding-top:5px;">The Properties tab now shows different icons for the different property types.</li><br />
<br />
<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><br />
<br />
<li style="padding-top:5px;">Web links are now opened in a new browser window.</li><br />
<br />
<li style="padding-top:5px;">Better logging in the Servlet container and Protege server logs if something goes wrong.</li><br />
<br />
<li style="padding-top:5px;">If running in external server mode, WebProtege will cleanly handle situations in which the Protege server becomes unavailable.</li><br />
<br />
<li style="padding-top:5px;">RPC calls are now available for creating/deleting classes and setting property values.</li><br />
<br />
<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><br />
</ul><br />
<br />
=== Build 103 - August 1, 2009 ===<br />
If running in external server mode, WebProtege is now compatible with the Protege 3.4.1 release.<br />
<br />
=== Build 102 - April 3, 2009 ===<br />
If running in external server mode, WebProtege is now compatible with the Protege 3.4 release.<br />
<br />
=== Build 101 - October 26, 2008 ===<br />
Initial 0.5 alpha release<br />
<br />
[[Category:WebProtege documentation]]</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=ProtegeQAGuide&diff=13782ProtegeQAGuide2022-02-14T19:24:42Z<p>Samsontu: </p>
<hr />
<div>This is the start page on how to (automatically) build and test all applications/projects related to Protégé.<br />
<br />
=Guidance Documents=<br />
[[File:infrastructure-2.png|thumb|Infrastructure with all servers and information flow]]<br />
<br />
{| border="1"<br />
| On the <span style="font-variant:small-caps;font-size:1.3em;font-weight:bold">[[Stanford:OverviewPage|Overview Page]]</span><br />
you find <br />
* some background information describing the rationale for caring about automated builds and testing and for establishing a corresponding infrastructure. <br />
* an overview chart displaying the entire infrastructure landscape. <br />
* a short description of all the relevant tools and the rationale for chosing the selected ones<br />
<br />
| The <span style="font-variant:small-caps;font-size:1.3em;font-weight:bold">[[Stanford:AdministratorGuide|Administrator Guide (Obsolete)]]</span> (&rarr; Alex) <br />
describes how to install and operate all the servers, among those:<br />
* Nexus repository: bmir-hudson1.stanford.edu/nexus<br />
* Hudson Build Sever (build statistics, administration of jobs): bmir-hudson1.stanford.edu <br />
* Sonar Server (code and architecture metrics, coverage reports and more): bmir-hudson1.stanford.edu/sonar (use link from Hudson to Sonar reports instead)<br />
* Tomcat Server (automated UI testing, not of general interest): bmir-hudson1.stanford.edu:8080<br />
* SVN-Repository: http://smi-protege.stanford.edu/repos/protege/<br />
<br />
|-<br />
| The <span style="font-variant:small-caps;font-size:1.3em;font-weight:bold">[[Stanford:DeveloperGuide|Developer Guide]]</span> (&rarr; external and Stanford internal)<br />
is the main page for developers. On these pages developers get answers to questions like<br />
* How do I initially set up my tools to work with one or more of the Protégé projects? <br />
* <strong>New:</strong> Please watch video tutorial.<br />
* How do I write test cases?<br />
* How do I get the lastest downloads?<br />
<br />
| The <span style="font-variant:small-caps;font-size:1.3em;font-weight:bold">[[Stanford:QaGuide|QA & Project Manager Guide]]</span> (&rarr; Tania, Jennifer, Tim &amp; other)<br />
is the address for everybody interested in the success and quality of builds and code. It gives explanations like<br />
* How to write/adjust the pom.xml?<br />
* What do these metrics tell me?<br />
* What do I have to do in order to add artifacts (e.g. jar-files) to my repository<br />
|}<br />
<br />
=Contact and further Information=<br />
The selection, installation and testing of the infrastructure as well as the initial transistion from traditional ANT-based to Maven based projects was done by [mailto://c.faigle@gmx.net Christian Faigle] and [mailto://mail@johner.org Christian Johner]. Please contact either for questions related to<br />
* Selection of tools<br />
* Administration of tools<br />
* Converting projects to MAVEN<br />
* Interpretation and adaptation of reports<br />
<br />
This page originally was written by [mailto://christian@johner.org Christian Johner], [http://www.johner-institut.de Institute for Healthcare IT].<br />
<br />
The [[Stanford:ToDoPage|Todos]] (for Christian, Alex)</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Protege_Ontology_Library&diff=13781Protege Ontology Library2022-02-14T18:40:08Z<p>Samsontu: Replaced content with "__NOTOC__
<div style="background:#F0E6CA; border:1px solid #AE5B08; padding:10px 15px 10px 20px; margin:2em 0 0 0;">
=== The Protege Ontology Library is no longer being ma..."</p>
<hr />
<div>__NOTOC__<br />
<div style="background:#F0E6CA; border:1px solid #AE5B08; padding:10px 15px 10px 20px; margin:2em 0 0 0;"><br />
=== The Protege Ontology Library is no longer being maintained. For biomedical ontologies, please visit<br />
[https://bioportal.bioontology.org BioPortal] ===<br />
<br />
<br />
<br />
</div><br /></div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Protege_Ontology_Library&diff=13780Protege Ontology Library2022-02-14T18:34:37Z<p>Samsontu: /* Welcome to the Protege Ontology Library! */ (checkpoint save)</p>
<hr />
<div>__NOTOC__<br />
<div style="background:#F0E6CA; border:1px solid #AE5B08; padding:10px 15px 10px 20px; margin:2em 0 0 0;"><br />
=== Welcome to the Protege Ontology Library! ===<br />
<br />
<!--<br />
This page is organized into the following groupings:<br />
<br />
* [[#OWL_ontologies|OWL ontologies]]<br />
* [[#Frame-based_ontologies|Frame-based ontologies]]<br />
* [[#Other_ontology_formats|Ontologies in other formats (e.g., DAML+OIL, RDF Schema, etc.)]]<br />
<br />
If your ontology is available in multiple formats, please feel free to link to it from multiple sections.<br />
<br />
''Please make insertions in alphabetical order. Thank you !!!''<br />
</div><br /><br />
--><br />
<br />
== OWL ontologies ==<br />
<br />
Information on how to open OWL files from the [http://protege.stanford.edu/overview/protege-owl.html Protege-OWL editor] is available on the main Protege Web site. See the [http://protege.stanford.edu/doc/owl/getting-started.html#creating_loading Creating and Loading Projects] section of the [http://protege.stanford.edu/doc/owl/getting-started.html Getting Started with Protege-OWL] Web page. Other ways to search for OWL ontologies include using Google: http://www.google.com/search?q=filetype:owl+owl, or the new Semantic Web search engine called [http://swoogle.umbc.edu/ Swoogle].<br /><br /><br />
<br />
<br />
* [http://www.aimatshape.net/resources/aas-ontologies AIM@SHAPE Ontologies]: Ontologies pertaining to digital shapes. Source: [http://www.aimatshape.net/ AIM@SHAPE NoE] - Advanced and Innovative Models And Tools for the development of Semantic-based systems for Handling, Acquiring, and Processing knowledge Embedded in multidimensional digital objects.<br />
<br />
* [http://www.isibang.ac.in/~bisu/ontology/instOntology.owl Institutional ontology]: Institutional Ontology is a model of a University/ Institute. This ontology is based on OWL-DL. Few instances are included to check its performance. Also, a file called [http://www.isibang.ac.in/~bisu/ontology/ instOntology_query_set.txt] containing a list of queries is provided. Contributed by [mailto:bisu@drtc.isibang.ac.in Biswanath Dutta][http://www.isibang.ac.in/~bisu/ DRTC, Bangalore].<br />
<br />
* [http://www.isibang.ac.in/~bisu/ontology/mod-ontology-09092016.owl MOD Ontology]: MOD stands for Metadata for Ontology Description and publication. MOD proposes a set of metadata elements which can be used to describe the ontologies, for instance, in ontology libraries and repositories. Like any other resources, ontologies also need to be described. The proper descriptions of the ontologies will enable us in discovering, identifying and selecting the right ontologies from the ontological libraries, and repositories. The details of this ontology can be found [http://dcpapers.dublincore.org/pubs/article/viewFile/3758/1948 here]. Contributed by [mailto:bisu@drtc.isibang.ac.in Biswanath Dutta] [http://www.isibang.ac.in/~bisu/ DRTC, Bangalore]. <br />
<br />
* [http://www.co-ode.org/ontologies/amino-acid/2005/10/11/amino-acid.owl amino-acid.owl]: A small OWL ontology of amino acids and their properties. Source: [http://www.co-ode.org/ontologies/amino-acid/2005/10/11/ Amino Acid Ontology Web site].<br />
<br />
* [http://www.ifomis.uni-saarland.de/bfo/ Basic Formal Ontology (BFO)]<br />
<br />
* [http://transontology.org/bhakti_gaudiya/bhakti.owl bhakti.owl]: An OWL ontology for the transcendental states of consciousness experienced by practitioners of bhakti-yoga, a form of Vedic consciousness engineering.<br />
<br />
* [http://dumontierlab.com/?page=ontologies Biochemical Ontologies]: Over 30 ontologies for knowledge representation and reasoning across scientific domains. Ontologies are normalized into non-disjoint primitive skeletons and complex class expressions for DL reasoning. Ontologies describe atoms, bonds, molecules, macromolecules and the processes they participate in.<br />
<br />
* [http://www.biopax.org/ BioPAX]: An OWL ontology for biological pathways, which is primarily used to exchange data between pathway resources.<br />
<br />
* [http://www.nbirn.net/birnlex/ BIRNLex]: An ontology created by and for the [http://www.nbirn.net/ Biomedical Informatics Research Network (BIRN)] in order to provide a shared semantic framework in which to annotate BIRN data related to multi-resolutional, cross-species studies of neurodegenerative disease. BIRNLex follows the OBO Foundry best practices and makes use of other OWL-based OBO ontologies.<br />
<br />
* [http://acl.icnet.uk/~mw BreastCancerOntology]: An OWL ontology for describing some features of Breast Cancer; Basic model is stable, but still being fleshed out.<br />
<br />
* [http://protege.cim3.net/file/pub/ontologies/camera/camera.owl camera.owl]: An OWL ontology about the individual parts of a photo camera. Source: [http://www.xfront.com/ XFront OWL Tutorial].<br />
<br />
* [http://www.bltk.ru/OWL/camera2.owl camera2.owl]: An improved OWL camera ontology based on above one from Roger L. Costello. Contributed by [mailto:igor_bessmertny@hotmail.com Igor Bessmertnyy].<br />
<br />
* [http://www.owl-ontologies.com/Cardiology.owl Cardiology.owl]: An ontology to present various cardiology diseases, their symptoms, tests, and complications. Contributed by Rishi.<br />
<br />
* [http://www.cellcycleontology.org/ Cell Cycle Ontology (CCO)]: An application ontology for the cell cycle process.<br />
<br />
* [https://github.com/CompGuideRepository/CompGuide-Editor/blob/master/Cguide.owl CompGuide Ontology Model]: The CompGuide ontology presents a formalisation of guidelines as linked lists of tasks, thus following the Task Network Model (TNM), representing Clinical Practice Guidelines as workflows.<br />
<br />
* [http://kt.ijs.si/software/CNOntology/cno.html CN Ontology]: An OWL ontology presenting the concepts used in collaborative networked organizations with focus on Virtual Organizations Breeding Environment.<br />
<br />
* [http://transontology.org/consciousness/consciousness1.owl consciousness1.owl]: An OWL ontology showing the transcendental background for consciousness according to the ancient Vedic literature.<br />
<br />
* [http://www.bpiresearch.com/BPMO/2004/03/03/cdl/Countries countries.owl]: The ISO 3166 Code List of countries. Contributed by [http://www.jenzundpartner.de/index.htm Dieter E. Jenz].<br />
<br />
*[https://github.com/ayesha-banu79/Owl-Ontology/blob/master/College%20Mngt%20Sys.owl CMS Ontology]:CMS stands for College Management System. This ontology describes all the majors concepts involved in management of any college. The details available at [http://dl.acm.org/citation.cfm?id=2393248].Contributed by Ayesha Banu.<br />
<br />
* [https://mywebspace.wisc.edu/jpthielman/web/DaycareOntology.htm Daycare.swrl.owl]: A demo ontology about a childcare center showing the use of SWRL for reasoning. Contributed by [mailto:peace@wisc.edu Jane Peace].<br />
<br />
* [http://www.nada.kth.se/~mehrana/Delegation.owl Delegation Ontology]: An OWL ontology to describe delegation concepts in the context of Grid computing.<br />
<br />
* [http://www.ecs.soton.ac.uk/~aoj04r/resist.owl Dependable Systems Ontology]: Ontology about resilient and dependable systems including threats, failures, faults and errors as used in the [http://www.resist-noe.eu ReSIST] project.<br />
<br />
* [http://serdis.dis.ulpgc.es/~a013715/aic/ontologias/ Dietas]: Esto es una ontología en OWL no terminada que simula un dietista.<br />
<br />
* [http://dolce.semanticweb.org/ DOLCE]: The Dolce foundational ontology and its extensions provide a domain-independent framework to build ontologies on the basis of highly-reusable patterns. Contributed by [mailto:aldo.gangemi@istc.cnr.it Aldo Gangemi].<br />
<br />
* [http://education.state.mn.us/datadictionary/owl/Education.owl Education Ontology]: Ontology for the Minnesota Department of Education based on the National Information Exchange Model (NIEM) structures and ISO/IEC 11179 standards. This domain includes information about K-12 students, teachers, schools, districts, enrollments, assessments, USDA food and nutrition programs, and on-line courses. Includes approximately 400 data elements. A case study will be presented at the Semantic Technology conference in March 2006. Feedback -> http://www.danmccreary.com.<br />
<br />
* [http://trajano.us.es/%7Eisabel/EHR/ EHROntology]: An Electronic Health Records ontology based on openEHR work. Contributed by [http://trajano.us.es/%7Eisabel Isabel Roman Martinez].<br />
<br />
* [http://persons.iis.nsk.su/en/person/ponom/ontologies/ Einstein's riddle (Zebra puzzle)]: formulation of the puzzle in ALCOIF Description Logic, just classify the ontology in Protege and get a solution by clicking on individuals.<br />
<br />
* [http://www.csm.ornl.gov/~7lp/esg-owl/ESG1.1.owl ESG]: An ontology describing very large simulation datasets and related information for climate sciences such as those found in the [http://www.earthsystemgrid.org/ Earth System Grid] project. Contributed by [http://www.csm.ornl.gov/~7lp Line Pouchard].<br />
<br />
* [http://protege.cim3.net/file/pub/ontologies/family.swrl.owl/family.swrl.owl family.swrl.owl]: A SWRL/OWL demo ontology about family relationships . Contributed by Christine Golbreich.<br />
<br />
* [http://www.osera.gov/owl/2004/11/fea/FEA.owl Federal Enterprise Architecture Reference Model Ontology (FEA-RMO)]: Representation of Federal Enterprise Architecture in OWL.<br />
<br />
* [http://www.fadyart.com/ontologies/data/Finance.owl Finance]: an ontology on financial instruments, involved parties, processes and procedures in securtities handling. Contributed by [http://www.fadyart.com/financeOntologyEN.htm Eddy Vanderlinden].<br />
<br />
* [http://loki.cae.drexel.edu/~wbs/ontology/fgdc-csdgm.htm fgdc-csdgm.owl]: Ontology for Content Standard for Digital Geospatial Metadata (CSDGM) of Federal Geographic Data Committee (FGDC). Contributed by Akm Saiful Islam, Bora Beran, Volkan Yargici, and Michael Piasecki.<br />
<br />
* [http://www.l3s.de/%7Edolog/fsm/index.html fsm.owl]: A simple ontology for finite state machines. Contributed by [http://www.learninglab.de/~dolog/index2.html Peter Dolog].<br />
<br />
* [http://xmlns.com/foaf/spec/index.rdf FOAF Ontology]: An ontology describes people, the links between them and the things they create and do. Contributed by [http://xmlns.com/foaf/spec/ Dan Brickley and Libby Miller].<br />
<br />
* [http://www.onto-med.de/ontologies/gfo/ General Formal Ontology (GFO)] - A foundational ontology by [http://www.informatik.uni-leipzig.de/fk/pers/herre.html Dr.Heinrich Herre] and colleagues. This entry added to this Ontology Library by [https://scholar.google.com/citations?user=jTkGEiMAAAAJ&hl=en&oi=sra Robert Rovetto]<br />
<br />
* [http://protege.cim3.net/file/pub/ontologies/generations/generations.owl generations.owl]: An ontology about family relationships that demonstrates classification. Contributed by [http://www.cs.man.ac.uk/~horridgm Matthew Horridge].<br />
<br />
* [http://loki.cae.drexel.edu/~wbs/ontology/ Geographic Information Metadata - ISO 19115]: An ontology representing Geographic Information Metadata - (ISO 19115).<br />
<br />
* [http://loki.cae.drexel.edu/%7Ehow/HydrologicUnits/hu hu.owl]: A hierarchic division of hydrologic units. Contributed by [http://loki.cae.drexel.edu/%7Ehow/Hydrologic_Units_ontology.html Luis Bermudez].<br />
<br />
* [http://individual.utoronto.ca/hesham/DetailedResearch.htm Infrastructure Product Ontology]: An OWL ontology for utility infrastructure products, their attributes, mechanisms, and measures. Products span all five sectors of utilities (Water, Wastewater, Gas, Electricity, and Telecom).<br />
<br />
* [http://loki.cae.drexel.edu/%7Ewbs/ontology/list.htm iso-metadata.owl]: Several ISO Geographic Information Ontologies developed with the Protege-OWL editor. Contributed by Akm Saiful Islam, Bora Beran, Luis Bermudez, Stephane Fellah & Michael Piasecki.<br />
<br />
* [http://protege.cim3.net/file/pub/ontologies/ka/ka.owl ka.owl]: Defines concepts from academic research. Contributed by [http://www.cs.man.ac.uk/%7Ehorrocks/ Ian Horrocks].<br />
<br />
* [http://protege.cim3.net/file/pub/ontologies/koala/koala.owl koala.owl]: A simple ontology about humans and marsupials. Contributed by [http://www.knublauch.com/ Holger Knublauch].<br />
<br />
* [http://lifeeventontology.googlepages.com/leo.owl leo.owl]: A simple ontology about life events within e-Government. Contributed by [http://domen.cukjati.googlepages.com/home Domen Cukjati].<br />
<br />
*[https://github.com/ayesha-banu79/Owl-Ontology/blob/master/Library%20Ontology.owl Library Ontology]: This Library ontology includes all the major classes & subclass hierarchy,properties,characteristics,restrictions and instances of a Library Management System of any Educational Organization. The details of this ontology can be found at [http://link.springer.com/chapter/10.1007/978-3-642-31600-5_51#page-1]. Contributed by Ayesha Banu.<br />
<br />
* [http://www.estrellaproject.org/lkif-core LKIF Core]: A core ontology of basic legal concepts. Contributed by [http://www.leibnizcenter.org/users/rinke Rinke Hoekstra].<br />
<br />
* [https://sites.google.com/site/ontoworks/ontologies Mahabarata Ontology] — An ontology based on one of the epic stories of ancient India [http://en.wikipedia.org/wiki/Mahabharata Mahabarata]. This ontology is developed by ontology research team at AIDB lab, [http://www.cse.iitm.ac.in/ IIT-Madras]. Contributed by [mailto:mvsquare1729@gmail.com Vinu E.V] and [mailto:lifeisbeautiful.shree@gmail.com Subhashree S]. <br />
<br />
* [http://protegewiki.stanford.edu/images/d/de/Monetary_ontology_0.1d.zip Monetary_ontology_0.1d.zip]: A zipped Protégé project of an ontology for currency creation and use. Also contains an "owl". The objective is an active description of all forms of "money" from barter to clearing systems, from precious metal coinage to debt-based fiat. It is oriented towards designers of payment systems and community currency systems. Here is a preview [http://protegewiki.stanford.edu/images/b/b5/Monetary_ontology.gif GIF] image [http://protegewiki.stanford.edu/index.php/Image:Monetary_ontology.gif !] First begun 2008/05/04 and last updated [http://protegewiki.stanford.edu/index.php/Image:Monetary_ontology_0.1d.zip 2008/05/12]. [http://protegewiki.stanford.edu/index.php/Image:MonetaryOntology.zip v0.0] Contributed by [mailto:hmjbram-protege@yahoo.com Martin "Hasan" Bramwell]<br />
<br />
* [http://mged.sourceforge.net/ontologies/MGEDOntology.owl MGEDOntology.owl]: An ontology for microarray experiments in support of MAGE v.1. Source: [http://mged.sourceforge.net/ MGED Society].<br />
<br />
* [https://www.dropbox.com/s/zggljjp9jbmvpqr/MR-MPS-SW.owl MR-MPS-SW] : Enterprise Ontologies as a complementary tool to support the adoption of software process quality models. The model selected for this work was the Reference Model MPS for software development (RM-MPS-SW), which is part of the Brazilian Software Process Improvement Program (MPS.BR). The RM-MPS-SW was developed focusing micro, small and medium-sized enterprises (MSMEs), although it is completely suited to large organizations. In this context, this work presents a methodology for the ontology development on the levels G and F of the RM-MPS-SW. Concepts of the PMBOK (Project Management Body of Knowledge) are included to support adherence to its principle by software companies. The inclusion of BSC (Balanced Scorecard) indicators approximates the model with the strategic planning of the company. The intention is that this methodology can be used as a basis for the representation of the other MPS-SW levels and other software process models.<br />
<br />
* [ftp://ftp1.nci.nih.gov/pub/cacore/EVS/ NCI Thesaurus]: A huge ontology developed by the National Cancer Institute (NCI). Source: [http://ncicb.nci.nih.gov/organization/personnel/core/caBIO/technical_resources/guides/quick_start/core/EVS NCI Enterprise Vocabulary Services].<br />
<br />
* [http://protegewiki.stanford.edu/wiki/File:~Uploaded_DomainOntology-NMS.zip Communication Network] A domain ontology of the SNMP-managed TCP/IP-based communication network system. Contributed by Sameera Abar<br />
<br />
* [http://www.semanticbible.org/ntn/ntn-overview.html New Testament Names]: A semantic knowledge base describing named things (people, places, and other classes) in the New Testament, as well as their attributes and relationships. It includes both an ontology and a substantial amount of instance data. NTNames is part of [http://www.semanticbible.org/ SemanticBible.org].<br />
<br />
* [http://protege.cim3.net/file/pub/ontologies/not.galen/not-galen.owl not-galen.owl]: A selective adaptation made in 1995 of an early prototype GALEN model; content is not related to or representative of any current or historical OpenGALEN release. Contributed by [http://www.cs.man.ac.uk/%7Ehorrocks/ Ian Horrocks].<br />
<br />
* [http://ise.icu.ac.kr/Ontologies/office-env1.owl office-env1.owl],[http://ise.icu.ac.kr/Ontologies/office-env2.owl office-env2.owl]: Ontologies for office environment. Contributed by Prakash Kadel<br />
<br />
* [http://loki.cae.drexel.edu/~wbs/ontology/ogc-gml.htm OGC]: Ontology for Geography Markup Language (GML3.0) of Open GIS Consortium (OGC). Contributed by Contributors: Zafer Defne, Akm Saiful Islam and Michael Piasecki.<br />
<br />
* [http://www.tssg.org/public/ontologies/omg/mof/2004/MOF.owl OMG - Meta Object Facility]: Ontology representation of the [http://www.omg.org/mof/ OMG-MOF] generated from the OMG Specification (XMI).<br />
<br />
* [http://www.tssg.org/public/ontologies/omg/qvt/2005/QVT.owl OMG - MOF - Query, View, and Transformations]: Ontology representation of the [http://www.omg.org/technology/documents/modeling_spec_catalog.htm#MOF_QVT OMG-MOF-QVT] generated from the OMG Specification (XMI).<br />
<br />
* [http://www.tssg.org/public/ontologies/omg/odm/2006/odm_2006_04_03_kludge.owl OMG - Ontology Definition Metamodel (ODM)]: Ontology representation of the [http://www.omg.org/ontology/ OMG-ODM] generated from the OMG Specification (XMI).<br />
<br />
* [http://www.tssg.org/public/ontologies/omg/uml/2004/UML2-Super-MDL-041007.owl OMG - Unified Modeling Language (UML2)]: Ontology representation of the [http://www.omg.org/technology/documents/modeling_spec_catalog.htm#UML OMG-UML2] generated from the OMG Specification (XMI).<br />
<br />
* [http://protege.stanford.edu/ontologies/ontoClean/ontoCleanOntology.html OntoClean]: Representation of [http://portal.acm.org/citation.cfm?doid=503124.503150 OntoClean] meta-properties and corresponding constraints as a Protege ontology and a set of PAL constraints.<br />
<br />
* [http://www.ecolleg.org/trms/ontology.html OntoTool]: An ontology that is used to model Task and Tool features for project realization. This ontology contains essential concepts about the relationship between task and tool and frequently asked questions about tool identification.<br />
<br />
* [http://nmg.upc.edu/~mserrano/ontologies/OSM.htm OSM - Ontology for Support and Management]: An ontology that contains all constructs required for the various versions of the Ontology for Support and Management of pervasive services by using ontology-based policy mechanisms run by IST-Context project and the research extensions towards Onto-Context framework to demonstrate advantages when context information is used for controlling management operations.<br />
<br />
* [http://protege.cim3.net/file/pub/ontologies/people.pets/people+pets.owl people+pets.owl]: From the [http://www.cs.man.ac.uk/%7Ehorrocks/ISWC2003/Tutorial/ ISWC03 tutorial] on OWL by Sean Bechhofer, Ian Horrocks, and Peter Patel-Schneider.<br />
<br />
* [http://afrodita.rcub.bg.ac.yu/~gasevic/projects/PNO/ Petrinet Semantic Web Infrastructure]: Contributed by [http://www.sfu.ca/~dgasevic/ Dragan Gasevic].<br />
<br />
* [http://philosurfical.open.ac.uk/ontology/philosurfical.owl PhiloSurfical ontology]: An ontology which extends [http://cidoc.ics.forth.gr/ CIDOC-CRM] and describes various dimensions normally associated to the philosophical domain (people, documents, ideas, events). Contributed by [http://people.kmi.open.ac.uk/mikele/ Michele Pasin], in the context of the [http://philosurfical.open.ac.uk/index.html/ PhiloSURFical] project.<br />
<br />
* [http://www.co-ode.org/ontologies/ Pizzas]: The OWL ontology used in the Protege-OWL Tutorial. Contributed by [http://www.co-ode.org/ The CO-ODE Project].<br />
<br />
* [http://www.aifb.uni-karlsruhe.de/Forschungsgruppen/BIK/wi2007/PNOntology.owl Pr/T net Ontology]: An ontology for high-level Petri nets.<br />
<br />
* [http://ppontology.googlepages.com/ PPOntology]: An OWL ontology for cereal plant protection. Currently, it is developed to encompass the field of diagnosis and treatment of barley disorders.<br />
<br />
* [http://www.proteinontology.info/ Protein Ontology]: Protein Ontology or PO provides a unified vocabulary for capturing declarative knowledge about protein domain and to classify that knowledge to allow reasoning. Contributed by [http://www.amandeep.org/ Amandeep S. Sidhu].<br />
<br />
* [http://mav.inf.uth.gr/SWS4HPSC/software/sao/saontology/view/SaOn.owl SaOn-Software Application Ontology]: An example ontology for searching, retrieving and using software applications, components.<br />
<br />
* [http://protege.cim3.net/file/pub/ontologies/shuttle/shuttle-crew-ont.owl shuttle-crew-ont.owl]: An ontology about the crew from a space shuttle. Source: [http://orlando.drc.com/SemanticWeb/Topics/Ontology/Ontologies.htm Dynamic Research Corporation].<br />
<br />
* [http://www.loria.fr/~coulet/ontology/snpontology/version1.3/snpontology_full.owl SNP-Ontology]: An ontology to represent genomic variations, and related concepts. Contributed by [http://www.loria.fr/~coulet/ Adrien Coulet].<br />
<br />
* [http://www.jaist.ac.jp/~nitun/sort.htm Sort Ontology]: Sort ontology is a model of ontologies where ontological classes are represented as sorts with the principles of identity and individuation. The model consists of four meta-classes: <nowiki>TypeSort</nowiki>, <nowiki>QuasitypeSort</nowiki>, <nowiki>RoleSort</nowiki>, and <nowiki>PhaseSort</nowiki>. It is intended to enrich the semantics of ontological classes by embedding abstract-level domain independent knowledge (called meta-knowledge) into OWL ontologies.<br />
<br />
* [http://loki.cae.drexel.edu/%7Ewbs/ontology/model.htm Surface-Water-Model-Ontology]: An ontology for surface water and water quality models currently exists based on the list provided SMIC, US Geological Survey using Protege. Contributed by Akm Saiful Islam. <br />
<br />
* [http://www.uv.es/~agentes/SVECore.owl SVECore.owl]: A core ontology for developing 3D Semantic Virtual Environments and a simple Domain Specific Ontology for creating a virtual bar ([http://www.uv.es/~agentes/DSOBar.owl DSOBar.owl]). Contributed by [mailto:francisco.grimaldo@uv.es Francisco Grimaldo]. <br />
<br />
* [http://sweet.jpl.nasa.gov/ontology/ SWEET Ontologies]: A Semantic Web for Earth and Environmental Terminology. Source: [http://www.jpl.nasa.gov/index.html Jet Propulsion Laboratory].<br />
<br />
* [http://protege.cim3.net/file/pub/ontologies/tambis/tambis-full.owl tambis-full.owl]: A biological science ontology developed by the [http://imgproj.cs.man.ac.uk/tambis/ TAMBIS] project. Contributed by [http://www.cs.man.ac.uk/%7Ehorrocks/ Ian Horrocks].<br />
<br />
* [http://www.ecolleg.org/trms/ontology.html Tool and Task]: An ontology that is used to model Task and Tool features for project realization. Contributed by [mailto:marek@ciel.pl Marek Szlezak].<br />
<br />
* [http://protege.cim3.net/file/pub/ontologies/travel/travel.owl travel.owl]: A tutorial OWL ontology for a Semantic Web of tourism. Contributed by Holger Knublauch.<br />
<br />
* [http://www.semanticweb.org/ontologies/2014/8/22/Toys.owl Toys.owl]: Toys are classified into various categories in Toys ontology.Contributed by Ayesha Ameen, Khaleel Ur Rahman Khan,B.Padmaja Rani [a.ameen@deccancollege.ac.in ] <br />
<br />
* [http://ontology.com.br/ Unified Foundational Ontology (UFO)] - A foundational ontology developed by [https://scholar.google.com/citations?user=nnfVBt8AAAAJ Dr.Giancarlo Guizzardi]. See also http://dev.nemo.inf.ufes.br/seon/UFO.html. This entry added to this Ontology Library by [https://scholar.google.com/citations?user=jTkGEiMAAAAJ&hl=en&oi=sra Robert Rovetto]<br />
<br />
* [http://www.semanticweb.org/ontologies/2012/5/Ontology1339825779701.owl University Ontology.owl]: University Ontology contains the details of working of university. Special focus is given to various courses offered by university.Object properties and data types properties are created for further understanding.Restrictions are added for pursuing a course of study depending on the current course of student.Contributed by Ayesha Ameen, Khaleel Ur Rahman Khan,B.Padmaja Rani [a.ameen@deccancollege.ac.in ]<br />
<br />
* [http://lsi.ugr.es/joseluisgs/videojuegos.owl Videogame's Elements Ontology]: A [http://lsi.ugr.es/joseluisgs/videojuegos/ videogame's elements ontology] that is used to model different videogame's properties like playability. Contributed by [mailto:joseluisgs@ugr.es José Luis González] University of Granada, Spain.<br />
<br />
* [http://www.cs.upc.edu/~loliva/OntoWAWO+.owl WaWo+ - Wastewater Ontology | Urban Water Systems]: An OWL ontology to represent knowledge in the domain of Urban Water Systems. Developed by [https://kemlg.upc.edu/ KEMLg] and [http://www.udg.edu/tabid/5486/Default.aspx?grup=GRCT0044 LEQUIA]. Contact: [mailto:loliva@cs.upc.edu Luis Oliva].<br />
<br />
* [http://www-ist.massey.ac.nz/wop/ WebOfPatterns]: An OWL ontology for object-oriented software design. Used to represent design patterns, a Java client exists that can download these descriptions and scan code for pattern instances.<br />
<br />
* [http://protege.cim3.net/file/pub/ontologies/wine/wine.owl wine.owl]: An ontology of wines (demonstrates project inclusion). Original source: [http://www.w3.org/TR/owl-guide/wine.rdf WebOnt OWL Guide].<br />
<br />
* [http://www.geocities.com/mdabulaish/woodontology/ Wood Ontology] — Contributed by [mailto:mdabulaish@rediffmail.com Muhammad Abulaish] and [mailto:lipika@maths.iitd.ernet.in Lipika Dey]. <br />
<br />
* [http://download.hozo.jp/onto_library/upperOnto.htm YAMATO: Yet Another More Advanced Top-level Ontology] - A foundational (top-level) ontology by [https://scholar.google.com/citations?user=8vYF2UIAAAAJ&hl=en Dr. Riichiro Mizoguchi] et al. It is freely available, in both a proprietary format used in the [http://www.hozo.jp/ HOZO Ontology Editor] ([https://scholar.google.com/citations?user=ppDfjoIAAAAJ&hl=en Dr.Kouji Kozaki]) and in OWL. This entry added to this Ontology Library by [https://scholar.google.com/citations?user=jTkGEiMAAAAJ&hl=en&oi=sra Robert Rovetto]<br />
<br /><br />
<br />
== Frame-based ontologies ==<br />
<br />
In the context of this page, the phrase "frame-based ontologies" loosely refers to ontologies that were developed using the [http://protege.stanford.edu/overview/protege-frames.html Protege-Frames editor]. For more information on how to open an ontology from the Protege-Frames editor, see the [http://protege.stanford.edu/doc/users_guide/index.html Protege-Frames User's Guide].<br /><br /><br />
<br />
* [http://mis.hevra.haifa.ac.il/~morpeleg/NewProcessModel/Malaria_PN_Example_Files.html Biological Processes]: A knowledge model of biological processes and functions that is graphical, for human comprehension, and machine-interpretable, to allow reasoning.<br />
<br />
* [http://www.umweltbundesamt.at/umweltdaten/schnittstellen/cedex/cedex_protege/?&tempL=1 CEDEX]: Representation of CEDEX in Protege. CEDEX is a base ontology for exchange and distributed use of ecological data.<br />
<br />
* [http://protege.cim3.net/cgi-bin/wiki.pl?DublinCoreProtegeOntology Dublin Core]: Representation of [http://dublincore.org/ Dublin Core] metadata in Protege.<br />
<br />
* [[Engineering ontologies]]: A set of ontologies for representing systems, their decomposition, connections, requirements and constraints<br />
<br />
* [http://www.bioinf.mdc-berlin.de/~schober/GandrIntro/ GandrKB (Gene annotation data representation)]: An ontology and knowledge base describing gene functions enabling biologists to annotate (multiple) genes on Affymetrix Microarrays per simple drag and drop. Annotation-concepts and genes can be linked for fast and intuitive context-exploration and extensive querying. Generated gene annotations can be interactively explored as semantic networks with advanced visualisation tools. Contributed by Daniel Schober.<br />
<br />
* GeneOntologyInProtege: Knowledge acquisition, consistency checking, and concurrency control in Gene Ontology.<br />
<br />
* [http://www.smi.stanford.edu/projects/intermed-web/guidelines/Protege_Ontology.htm Guideline Interchange Format (GLIF)]: Representation of [http://www.glif.org/ GLIF] in Protege.<br />
<br />
* [http://protege.stanford.edu/ontologies/HL7RIM/index.html Health Level 7 Data Types and Top-Level RIM Classes]: A Protege representation of the [http://www.hl7.org/ HL7] version 3 data types and top-level classes of the Reference Information Model. Contributed by [http://www.stanford.edu/~swt/ Samson Tu].<br />
<br />
* [http://www.klinikum.uni-heidelberg.de/Englische-Version-Promotionsarbeiten.8915.0.html#c17816 HELEN]: The HELEN Guideline representation ontology.<br />
<br />
* [http://www.ics.mq.edu.au/~borgun/Software.html HL7-RIM]: HL7-RIM as a Protege ontology. Contributed by Bhavna Orgun.<br />
<br />
* [http://nets.ii.uam.es/neptuno/iptc/ IPTC Subject Reference System]: RDF Schema and Protege ontology representations of the Subject Reference System.<br />
<br />
* [http://protege.stanford.edu/ontologies/ontoClean/ontoCleanOntology.html OntoClean]: Representation of [http://portal.acm.org/citation.cfm?doid=503124.503150 OntoClean] meta-properties and corresponding constraints as a Protege ontology and a set of PAL constraints.<br />
<br />
* [http://pcontology.et.ntust.edu.tw/ Personal Computer - Do It Yourself (PC-DIY)]: An ontology which contains essential concepts about the personal computer and frequently asked questions about Personal Computer - Do It Yourself.<br />
<br />
* [http://www.getopt.org/ecimf/contrib/onto/REA/index.html Resource-Event-Agent Enterprise (REA)]: An ontology that is used to model economic aspects of e-business frameworks (e.g. in ebXML) and enterprise information systems.<br />
<br />
* [http://protege.stanford.edu/ontologies/ontologyOfScience/ontology_of_science.htm Science Ontology]: A modified version of the KA² ontology describing research-related information.<br />
<br />
* [http://protege.cim3.net/cgi-bin/wiki.pl?SuggestedUpperMergedOntology Suggested Upper Merged Ontology (SUMO)]: An ontology developed within the [http://suo.ieee.org/ IEEE Standard Upper Ontology Working Group] with the goal of developing a standard ontology that will promote data interoperability, information search and retrieval, automated inferencing, and natural language processing.<br />
<br />
* [http://protege.stanford.edu/plugins/psmtab/upml_editor.html The Uniform Problem-solving Method development Language (UPML)]: An ontology and editor for modeling libraries of reusable (i.e., generic and adaptable) components of knowledge-based systems, namely tasks, problem-solving methods and domain models.<br />
<br />
* [http://drtc.isibang.ac.in/~bisu/ontology/instOntology.owl Instituto Kuluwulu]: This is a model to check the reliability of the Wiki Ontology Library. Sorry for this, but we had to do it XD. Por favor no tomen represalias, solo somos estudiantes con ganas de chequear este wiki. We love ontologies.<br />
<br />
<br /><br /><br />
<br />
== Other ontology formats ==<br />
<br />
* [http://protege.cim3.net/cgi-bin/wiki.pl?DublinCoreProtegeOntology Dublin Core]: Representation of [http://dublincore.org/ Dublin Core] metadata in Protege.<br />
<br />
* [http://www.ics.mq.edu.au/~borgun/Software.html HL7-RIM]: HL7-RIM as a Protege ontology. Contributed by Bhavna Orgun.<br />
<br />
* [http://nets.ii.uam.es/neptuno/iptc/ IPTC Subject Reference System]: RDF Schema and Protege ontology representations of the Subject Reference System.<br />
<br />
* [http://www.learninglab.de/~dolog/learnerrdfbindings/ Learner]: An ontology describing Learner features used for personalization in eLearning systems. Created in the context of EU/IST project [http://www.elena-project.org/ Elena].<br />
<br />
* [http://www.ontology.org.il Multi-dimensional Proverb ontology]: An ontology of Hebrew Proverbs by Maayan Zhitomirsky-Geffet, Gila Prebor and Orna Bloch from Information Science dept., Bar-Ilan university, Ramat-Gan, Israel.<br />
<br />
* [http://afrodita.rcub.bg.ac.yu/%7Egasevic/projects/PNO Petrinet Semantic Web Infrastructure]: Contributed by Dragan Gasevic.<br />
<br />
* [http://www.getopt.org/ecimf/contrib/onto/REA/index.html Resource-Event-Agent Enterprise (REA)]: An ontology that is used to model economic aspects of e-business frameworks (e.g., in ebXML) and enterprise information systems.<br />
<br />
* [http://www.cs.vu.nl/~mcaklein/unspsc/ Universal Standard Products and Services Classification (UNSPSC)]: A coding system to classify both products and services for use throughout the global marketplace.<br />
<br />
* [https://www.cyc.com/archives/service/cyc-knowledge-base CyC Ontology / OpenCyc / CyC Knowledge Base]: https://www.cyc.com/</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=WebProtegeUsersGuide&diff=13779WebProtegeUsersGuide2022-02-09T21:46:24Z<p>Samsontu: </p>
<hr />
<div><p style="padding:0; margin:0; font-size:1.9em; font-weight:bold; word-spacing:-2px;">WebProtégé User Guide</p><br />
<br />
<br />
'''WebProtégé''' is an open source, lightweight, web-based ontology editor.<br />
<br />
<br />
__TOC__<br />
<br />
'''Looking for the user guide of the old WebProtege (release 1.0)? [[WebProtege1.0UsersGuide|Here it is]].'''<br />
<br />
'''Go back to [[WebProtege|WebProtégé main page]].'''<br />
<br />
<br />
= Screencasts =<br />
<br />
[[File:WP-screencast.png|thumb|70px|left|link=http://www.youtube.com/watch?v=QvURiHVXnQQ]]<br />
<br />
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.).<br />
<br />
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].<br />
<br />
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]. <br />
<br />
<br />
= Home Screen =<br />
<br />
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.<br />
<br />
[[File:wp-home-screen.png|800px]]<br />
<br />
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).<br />
<br />
== Nav Bar ==<br />
<br />
[[File:Wp-nav-bar.png]]<br />
<br />
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.<br />
<br />
== Creating and Uploading Projects ==<br />
<br />
[[File:wp-project-action-buttons.png]]<br />
<br />
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.<br />
<br />
[[File:wp-upload-dialog.png]]<br />
<br />
== Sharing Project with Collaborators ==<br />
<br />
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.<br />
<br />
[[File:wp-sharing-settings.png]]<br />
<br />
<br />
= Lightweight editing with auto-completion support =<br />
<br />
It is now much easier and faster to create content in the new interface of WebProtege that has support for auto-completion. <br />
<br />
[[File:WP-classes.png|800px]]<br />
<br />
<br />
= Collaboration support =<br />
<br />
The Changes portlet shows the changes associated to an entity in the ontology. The change tracking provide a full and executable change history.<br />
<br />
[[File:WP-changes.png|800px]]<br />
<br />
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.<br />
<br />
[[File:WP-dashboard.png|800px]]<br />
<br />
= Viewing and Editing OWL 2 Ontologies = <br />
<br />
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.<br />
<br />
[[File:Add-content-2.png]]<br />
<br />
<br />
WebProtégé currently contains the following OWL 2 specific portlets, the '''OWL Entity Description Browser''' and the '''OWL Entity Description Editor'''.<br />
<br />
== The OWL Entity Description Browser ==<br />
<br />
'''OWL Entity Description Browser''' - 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].<br />
<br />
[[File:cephalapod-example.png]]<br />
<br />
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.<br />
<br />
[[File:cephalapod-property-example.png]]<br />
<br />
As shown in the Figure below, axiom annotations are shown as indented annotations (a slightly more compact form of the Manchester Syntax).<br />
<br />
[[File:axiom-annotations-example.png]]<br />
<br />
<br />
== The OWL Entity Description Editor ==<br />
<br />
This portlet supports the complete editing of OWL 2 ontologies. It provides a Manchester Syntax text editor, with syntax highlighting, error checking and autocompletion. The '''OWL Entity Description Editor''' portlet and can be added to tabs that permit editing of classes, properties and individuals. For projects that contain multiple ontologies, the editor also makes it possible to tell which ontology axioms reside in. Finally, it is possible to bundle multiple edits for a given entity together and "commit" them with an optional comment. <br />
<br />
[[File:owl_entity_editor_1.png]]<br />
<br />
[[File:owl-entity-editor-2.png]]<br />
<br />
[[File:owl-entity-editor-3.png]]<br />
<br />
<br />
= Ontologies with imports =<br />
<br />
Ontologies with imports can be uploaded to WebProtege. If an import is available at the imported URL, then WebProtege will fetch it from there.<br />
<br />
However, it is also possible to have local imports that are not resolvable at the import URL, but which are provided as additional files (similar to how Protege desktop handles local imports).<br />
<br />
To upload to WebProtege an ontology with local imports, create a zip archive, which should contain:<br />
* the top ontology (most importing one), which needs to be renamed to <code>root-ontology.owl</code>, and<br />
* the imported OWL files.<br />
<br />
The zip archive can be uploaded to WebProtege through the ''Upload Projects'' button, and WebProtege will be able to read the local imports from the archive.<br />
<br />
<br />
= Rules support =<br />
<br />
It is possible to view and edit rules in WebProtege using the [[WebProtegeUsersGuide#The_OWL_Entity_Description_Editor|OWL Entity Description Editor]]. The rules are shown in the ''Rule'' section:<br />
<br />
[[File:SwrlWP1.png|600px]]<br />
<br />
<br />
The editing of rules uses auto-completion for the entities in the ontology and for swrl builtins:<br />
<br />
[[File:SwrlWP2.png|600px]]<br />
<br />
<br />
= Other tabs and portlets =<br />
<br />
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]].<br />
<br />
= References =<br />
<br />
Further documentation and references on WebProtégé can be found [[WebProtege#References|here]].<br />
<br />
<br />
'''Go back to [[WebProtege|WebProtégé main page]].'''<br />
<br />
[[Category:WebProtege documentation]]</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=WebProtegeUsersGuide&diff=13778WebProtegeUsersGuide2022-02-09T21:45:55Z<p>Samsontu: </p>
<hr />
<div><p style="padding:0; margin:0; font-size:1.9em; font-weight:bold; word-spacing:-2px;">WebProtégé User Guide</p><br />
<br />
<br />
'''WebProtégé''' is an open source, lightweight, web-based ontology editor.<br />
<br />
<br />
__TOC__<br />
<br />
'''Looking for the user guide of the old WebProtege (release 1.0)? [[WebProtege1.0UsersGuide|Here it is]].'''<br />
<br />
'''Go back to [[WebProtege|WebProtégé main page]].'''<br />
<br />
<br />
= Screencasts =<br />
<br />
[[File:WP-screencast.png|thumb|70px|left|link=http://www.youtube.com/watch?v=QvURiHVXnQQ]]<br />
<br />
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.).<br />
<br />
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].<br />
<br />
<! -- 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]. --><br />
<br />
<br />
= Home Screen =<br />
<br />
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.<br />
<br />
[[File:wp-home-screen.png|800px]]<br />
<br />
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).<br />
<br />
== Nav Bar ==<br />
<br />
[[File:Wp-nav-bar.png]]<br />
<br />
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.<br />
<br />
== Creating and Uploading Projects ==<br />
<br />
[[File:wp-project-action-buttons.png]]<br />
<br />
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.<br />
<br />
[[File:wp-upload-dialog.png]]<br />
<br />
== Sharing Project with Collaborators ==<br />
<br />
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.<br />
<br />
[[File:wp-sharing-settings.png]]<br />
<br />
<br />
= Lightweight editing with auto-completion support =<br />
<br />
It is now much easier and faster to create content in the new interface of WebProtege that has support for auto-completion. <br />
<br />
[[File:WP-classes.png|800px]]<br />
<br />
<br />
= Collaboration support =<br />
<br />
The Changes portlet shows the changes associated to an entity in the ontology. The change tracking provide a full and executable change history.<br />
<br />
[[File:WP-changes.png|800px]]<br />
<br />
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.<br />
<br />
[[File:WP-dashboard.png|800px]]<br />
<br />
= Viewing and Editing OWL 2 Ontologies = <br />
<br />
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.<br />
<br />
[[File:Add-content-2.png]]<br />
<br />
<br />
WebProtégé currently contains the following OWL 2 specific portlets, the '''OWL Entity Description Browser''' and the '''OWL Entity Description Editor'''.<br />
<br />
== The OWL Entity Description Browser ==<br />
<br />
'''OWL Entity Description Browser''' - 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].<br />
<br />
[[File:cephalapod-example.png]]<br />
<br />
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.<br />
<br />
[[File:cephalapod-property-example.png]]<br />
<br />
As shown in the Figure below, axiom annotations are shown as indented annotations (a slightly more compact form of the Manchester Syntax).<br />
<br />
[[File:axiom-annotations-example.png]]<br />
<br />
<br />
== The OWL Entity Description Editor ==<br />
<br />
This portlet supports the complete editing of OWL 2 ontologies. It provides a Manchester Syntax text editor, with syntax highlighting, error checking and autocompletion. The '''OWL Entity Description Editor''' portlet and can be added to tabs that permit editing of classes, properties and individuals. For projects that contain multiple ontologies, the editor also makes it possible to tell which ontology axioms reside in. Finally, it is possible to bundle multiple edits for a given entity together and "commit" them with an optional comment. <br />
<br />
[[File:owl_entity_editor_1.png]]<br />
<br />
[[File:owl-entity-editor-2.png]]<br />
<br />
[[File:owl-entity-editor-3.png]]<br />
<br />
<br />
= Ontologies with imports =<br />
<br />
Ontologies with imports can be uploaded to WebProtege. If an import is available at the imported URL, then WebProtege will fetch it from there.<br />
<br />
However, it is also possible to have local imports that are not resolvable at the import URL, but which are provided as additional files (similar to how Protege desktop handles local imports).<br />
<br />
To upload to WebProtege an ontology with local imports, create a zip archive, which should contain:<br />
* the top ontology (most importing one), which needs to be renamed to <code>root-ontology.owl</code>, and<br />
* the imported OWL files.<br />
<br />
The zip archive can be uploaded to WebProtege through the ''Upload Projects'' button, and WebProtege will be able to read the local imports from the archive.<br />
<br />
<br />
= Rules support =<br />
<br />
It is possible to view and edit rules in WebProtege using the [[WebProtegeUsersGuide#The_OWL_Entity_Description_Editor|OWL Entity Description Editor]]. The rules are shown in the ''Rule'' section:<br />
<br />
[[File:SwrlWP1.png|600px]]<br />
<br />
<br />
The editing of rules uses auto-completion for the entities in the ontology and for swrl builtins:<br />
<br />
[[File:SwrlWP2.png|600px]]<br />
<br />
<br />
= Other tabs and portlets =<br />
<br />
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]].<br />
<br />
= References =<br />
<br />
Further documentation and references on WebProtégé can be found [[WebProtege#References|here]].<br />
<br />
<br />
'''Go back to [[WebProtege|WebProtégé main page]].'''<br />
<br />
[[Category:WebProtege documentation]]</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Install_Protege5&diff=13777Install Protege52021-12-23T20:15:13Z<p>Samsontu: </p>
<hr />
<div><br /><span style="font-weight:bold; font-size:20px;">Protege Desktop 5.x Installation Instructions</span><br /><br /><br />
<br />
<br />
__TOC__<br />
<br />
<br />
== Platform specific instructions ==<br />
<br />
Click on the links below for the platform specific instructions. The platforms-specific archives include the Java JRE, so it is not required to have Java installed on your machine. Use the platform-independent archive if you would like to use a specific version of Java, or if your system is 32-bit (the case with older computers).<br />
<br />
=== [[File:Win-logo.jpg|50px]] [[Instal_Protege5_Win|Windows]] === <br />
''Includes the JRE, and works for 64-bit Windows platforms''<br />
<br />
=== [[File:Mac-logo.jpg|50px]] [[Install_Protege5_Mac|Mac OSX]] ===<br />
''Includes the JRE, and works for 64-bit OSX platforms''<br />
<br />
=== [[File:Tux-logo.png|50px]] [[Install_Protege5_Linux|Linux]] ===<br />
''Includes the JRE, and works for 64-bit Linux platforms''<br />
<br />
=== [[File:PlatfIndep-logo.png|50px]] [[Install_Protege5_PlatformIndep|Platform Independent]] ===<br />
''Does not include the JRE, requires a Java version 8 or newer installed, works on any platform''<br />
<br />
<br />
== Troubleshooting ==<br />
<br />
''Q'': ''When I try to run Protege from the platform-independent archive with the run script, I get an <code>UnsupportedClassVersionError</code>, e.g., <code>"Exception in thread "main" java.lang.UnsupportedClassVersionError: Bad version number in .class file"</code>''<br />
<br />
''A'': Most likely you have an older Java version installed. Protege requires Java 8 or later. Please see the documentation above on how to check which version of Java is installed on your system.<br />
<br />
<br />
== How to get help ==<br />
<br />
If you have problems installing or running Protege Desktop, please refer to the [[Install_Protege5#Troubleshooting|troubleshooting]] section first. We also recommend searching the [http://protege-project.136.n4.nabble.com/ mailing list archives], as the problem and a solution might have already been posted. <br />
<br />
If you can't find the answers from these resources, send an email to the [http://protege.stanford.edu/support.php#mailingListSupport '''Protege User Support''' mailing list] (you need to be subscribed to post). Please be as specific as possible and try to include the following items:<br />
<br />
<br />
* What is your operating system (e.g., OS X 10.9, Windows 7, etc.)?<br />
* What is your Java version?<br />
* What are the specific steps to reproduce the problem?<br />
* Are there any error messages in the console window or the log file?<br />
* What is the observed behavior?<br />
<br />
<br />
The more detail you provide up front, the more helpful we can be in terms of a prompt response.</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=ProtegeDesktopUserDocs&diff=13776ProtegeDesktopUserDocs2021-12-22T22:19:54Z<p>Samsontu: </p>
<hr />
<div>= Protege Desktop User Documentation =<br />
<br />
This page is the official documentation home for the '''Protege Desktop application versions 4, 5 and higher'''. <br />
<br />
<br />
__TOC__<br />
<br />
<br />
== Build status & release notes ==<br />
<br />
The latest version of Protege Desktop is '''5.5''':<br />
<br />
* [https://github.com/protegeproject/protege-distribution/releases Release notes] <br />
* [[Install_Protege5|Installation instructions]]<br />
* [http://protege.stanford.edu/products.php#desktop-protege Download latest version of Protege]<br />
<br />
You may also download [[Protege_Desktop_Old_Versions|previous versions of Protege]] and read the complete list of release notes. Older Protege 5.0 beta release notes are available [[Protege_5.0_Beta_Release_Notes|here]].<br />
<br />
== Bugs & feature requests ==<br />
<br />
Before you report a bug or feature request, check the [http://protege-project.136.n4.nabble.com/ Protege mailing lists archives] to ensure it hasn't already been reported. If the item is not currently open or you have further information or a question about an existing item, please post a message on the [http://mailman.stanford.edu/mailman/listinfo/protege-user protege-user mailing list]. Give as much detail as possible (including examples or ontologies if possible) as this will help us track things down more quickly.<br />
<br />
Current GitHub issue tracker: https://github.com/protegeproject/protege/issues?state=open<br />
<br />
<br />
== Frequently asked questions ==<br />
<br />
We've put together a wiki page to answer the [[Protege-OWL_4_FAQ | most commonly asked questions]] about Protege Desktop.<br />
<br />
<br />
== Getting started / tutorials ==<br />
<br />
The Getting started and tutorials have been moved to the [[Main_Page|main page]] of the wiki.<br />
<br />
<br />
== Editor features ==<br />
<br />
* [[Protege4Features | Overview of features]] - a quick summary of the editor<br />
* [[Protege4Views | Protege views guide]] - a list of all of the default views that are distributed with Protege<br />
* [[Protege4Shortcuts | Protege menu guide]] - all of the default menus explained in detail (with keyboard shortcuts)<br />
* [[Protege4Preferences | Protege preferences guide]] - customizing Protege to your needs<br />
* [[Protege4NamingAndRendering|Naming and rendering of entities]] - a note on naming things in OWL and configuring Protege to support your naming conventions<br />
* [[Protege4ExpressionEditor | Protege expression editor]] - adding and editing OWL expressions in Protege<br />
* [[Manchester_OWL_Syntax|Manchester OWL Syntax]] - an overview of the default syntax used by Protege<br />
* [[DLQueryTab | DL Query tab]] - how to query using arbitrary class expressions in OWL<br />
* [[Importing_Ontologies_in_P41|OWL Imports]] - modular ontology support in OWL and Protege<br />
* [[Protege4AxiomAnnotations|Axiom annotations]] - how to annotate at axiom level in Protege <br />
* [[Protege4OWLDiff|Protege OWL Diff]] - compare two versions of an ontology<br />
<br />
== Advanced features ==<br />
<br />
* [[BeanShell | The Bean Shell]] - Making complex queries against an ontology.<br />
* [[Protege4ClientServer | The Protege 4 Server]]<br />
<br />
<br />
== Further setup / configuration ==<br />
<br />
* [[ChangingTheHeapSize|Adding more memory]]<br />
* [[EnablingDoubleClick|Double-clicking on OWL files]]<br />
* [[ClearingP4Preferences|Dealing with Protege preferences problems]]<br />
* [[Working with firewalls and proxies]]<br />
<br />
<br />
== Plugins ==<br />
<br />
=== Finding plug-ins ===<br />
<br />
* Protege will find plugins and updates for you. See our [[EnablePluginAutoUpdate|Auto Update]] page.<br />
<br />
* [[Protege-OWL_4.0 | Plugins for Protege]] - the list of all plugins compatible with different versions is available [[Protege_Plugin_Library|here]].<br />
<br />
* [https://github.com/co-ode-owl-plugins CO-ODE Protege Plugins] - the CO-ODE group at the University of Manchester is the biggest contributor of plug-ins to the Protege editor. The CO-ODE plugins that are compatible with your installation of Protege will show up when going in the File menu -> Check for plugins<br />
<br />
=== Advertising plug-ins ===<br />
<br />
If you have developed a plug-in for Protege and you would like to contribute it to the community,<br />
please see [[Protege4Contributing#Plugins|contributing plugins]].<br />
<br />
<br />
== Contributing ==<br />
<br />
Please see this page for details on how you can [[Protege4Contributing|contribute]].</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Setting_Heap_Size&diff=13775Setting Heap Size2021-12-22T22:12:12Z<p>Samsontu: </p>
<hr />
<div><span style="font-weight:bold;font-size:18px;">Setting the Heap Size</span><br />
<br />
<br />
<span style="font-weight:bold;font-size:16px;">Recommendations for setting the heap size (read first!)</span><br />
<br />
<br />
You must be careful about setting the heap size parameter. If you set it too low then you will get "out of memory" errors. If you set it too high then your system will hang or you will suffer poor performance because parts of the jvm will be swapped in and out of memory. A rule of thumb is that you should not set this parameter larger than about 80% of your free physical memory. On Windows XP machines you can determine your free physical memory from the Performance tab of the Task Manager application. On Mac machines, click the apple (upper left hand corner and "about this mac"). On Linux machines, you can use the wonderful proc filesystem and look at the meminfo "file".<br />
<br />
Boosting the heap size parameter will allow you to read in larger file-based projects. It will also improve the performance of the database back-end since more memory is available for caching.<br />
<br />
The most common source of very slow performance on older systems (or laptops) is having the heap size set too large. If your system does not have 100MB of free memory then even the Protege default value is too big and you should make it smaller (or buy more memory). <br />
<br />
The best way to know if you have succeeded in changing the memory settings is to look at the console when Protege starts up. Protege will print out the memory settings as they start. The console or the log during startup will look something like this:<br />
<pre><br />
INFO 11:34:25 ------------------------------------ Protege -----------------------------------<br />
INFO 11:34:25 Protege Desktop<br />
INFO 11:34:25 Version 5.5.0, Build <br />
INFO 11:34:25 <br />
INFO 11:34:25 <br />
INFO 11:34:25 ----------------------------------- Platform -----------------------------------<br />
INFO 11:34:25 Java: JVM 1.8.0_121-b13 Memory: 2237M<br />
INFO 11:34:25 Language: en, Country: US<br />
INFO 11:34:25 Framework: Apache Software Foundation (1.8) <br />
INFO 11:34:25 OS: macosx (10.16)<br />
INFO 11:34:25 Processor: x86-64<br />
<br />
</pre><br />
<br />
There are several ways of setting the heap size depending on how you run Protege. Note that for 64 bit windows machines there is a but in InstallAnywhere that prevents the user from setting the heap size over something like 1.5G. So in this case you will have to set up the run.bat script method of starting Protege.<br />
<br />
__TOC__<br />
<br />
<br />
==== Start Protege by Protege.exe/Protege or by double-cliking on the Protege icon (Windows/Linux) ====<br />
<br />
Michael DeBellis wrote on 2021/12/22:<br />
<br />
<start><br />
Needing more memory for Desktop Protege is a common issue and there is a simple solution. In the main directory where you have Protege [version 5.5 in 2021] there should be a file called Protege.I4J.ini That file is what Protege looks at when it starts up to determine how much memory Java can allocate. If you edit that file in Notepad or some other lightweight text processor it should currently look like this:<br />
<br />
-Xms200M<br />
-Xmx500M<br />
-Xss16M<br />
<br />
Xmx is the one you want to edit (I would recommend you make a copy of the original file first). That specifies the maximum amount of memory Protege can use. Xms is the initial memory that will be allocated and Xss defines the increments used when allocating more memory. The main thing to keep in mind is not to allocate so much memory that it starts to limit the performance of other programs which of course depends on how much memory your desktop or laptop have. <br />
<end><br />
<br />
For '''Protege 3.x''' you can do this in the Protege UI.<br />
* Go to '''File -> Preferences menu -> Protege.lax'''<br />
* Update the second column of the row containing <code>lax.nl.java.option.java.heap.size.max</code><br />
* Click on OK<br />
<br />
Please note that the changes take effect the next time you start Protege.<br />
<br />
Below is a screenshot of the Protege.lax panel.<br />
<br />
<br />
[[Image:Preferences-protege.lax.png]]<br />
<br />
<br />
For '''Protege 4''', you must edit directly the Protege.lax file in a text editor.<br />
<br />
Edit the following line in the Protege.lax file in the Protege installation directory:<br />
<br />
lax.nl.java.option.java.heap.size.max=100000000<br />
<br />
==== Start Protege by double-clicking on the Protege icon (Mac) ====<br />
<br />
If you run Protege on a Mac by double clicking an icon, you need to edit the Info.plist file that is hidden within that icon. Right click the icon (or ^-click for one button mouses) and click "show package contents". A new finder window will come up. Double click "Contents" and then "Info.plist". Traverse down the tree as follows: "Root" --> "Java" --> "JVMOptions". In JVMOptions edit the -Xmx line to indicate the correct memory usage. (Add the line <string>-Xmx2400M</string> if it's not there initially.)<br />
<key>JVMOptions</key><br />
<array><br />
<string>-Dapple.laf.useScreenMenuBar=true</string><br />
<string>-Xss16M</string><br />
<string>-Xms500M</string><br />
<string>-Xmx1400M</string><br />
<br />
<br />
==== Start Protege by double-clicking on the applescript file (Mac) ====<br />
<br />
If you run Protege on a Mac by double clicking the applescript file then you need to modify the -Xmx line in the script.<br />
<br />
<br />
==== Start Protege from the command line ====<br />
<br />
To run Protege from the command line, write in a terminal:<br />
<br />
.\run.sh<br />
<br />
(or, if on Windows, <code>run.bat</code>). You may change the heap size by editing the run script in a text editor, and change the value of the <code>-Xmx</code> argument. For example, to start with a 500MB heap size, use <code>-Xmx500M</code>. Read more on setting the heap size as an argument for generic Java applications [https://docs.oracle.com/javase/8/docs/technotes/tools/windows/java.html here] and [http://docs.oracle.com/javase/8/docs/technotes/guides/vm/gctuning/index.html here].<br />
<br />
Note that on Windows machines if you have installed the version of Protege that comes with its own jvm, you may need to change the path to java to jre\bin\java.exe. So for instance, to get 2G of heap space, you might change the Protege 4.2 run.bat file to be:<br />
<br />
<code>jre\bin\java.exe -Xmx2G -Dlog4j.configuration=file:log4j.xml -DentityExpansionLimit=100000000 -Dfile.encoding=utf-8 -Dorg.protege.plugin.dir=plugins -classpath bin/felix.jar;bin/ProtegeLauncher.jar org.protege.osgi.framework.Launcher</code><br />
<br />
<br />
[[Category:Protege documentation]]</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Setting_Heap_Size&diff=13774Setting Heap Size2021-12-22T22:10:37Z<p>Samsontu: /* Start Protege by Protege.exe/Protege or by double-cliking on the Protege icon (Windows/Linux) */</p>
<hr />
<div><span style="font-weight:bold;font-size:18px;">Setting the Heap Size</span><br />
<br />
<br />
<span style="font-weight:bold;font-size:16px;">Recommendations for setting the heap size (read first!)</span><br />
<br />
<br />
You must be careful about setting the heap size parameter. If you set it too low then you will get "out of memory" errors. If you set it too high then your system will hang or you will suffer poor performance because parts of the jvm will be swapped in and out of memory. A rule of thumb is that you should not set this parameter larger than about 80% of your free physical memory. On Windows XP machines you can determine your free physical memory from the Performance tab of the Task Manager application. On Mac machines, click the apple (upper left hand corner and "about this mac"). On Linux machines, you can use the wonderful proc filesystem and look at the meminfo "file".<br />
<br />
Boosting the heap size parameter will allow you to read in larger file-based projects. It will also improve the performance of the database back-end since more memory is available for caching.<br />
<br />
The most common source of very slow performance on older systems (or laptops) is having the heap size set too large. If your system does not have 100MB of free memory then even the Protege default value is too big and you should make it smaller (or buy more memory). <br />
<br />
The best way to know if you have succeeded in changing the memory settings is to look at the console when Protege starts up. Protege will print out the memory settings as they start. The console or the log during startup will look something like this:<br />
<pre><br />
INFO 11:34:25 ------------------------------------ Protege -----------------------------------<br />
INFO 11:34:25 Protege Desktop<br />
INFO 11:34:25 Version 5.5.0, Build <br />
INFO 11:34:25 <br />
INFO 11:34:25 <br />
INFO 11:34:25 ----------------------------------- Platform -----------------------------------<br />
INFO 11:34:25 Java: JVM 1.8.0_121-b13 Memory: 2237M<br />
INFO 11:34:25 Language: en, Country: US<br />
INFO 11:34:25 Framework: Apache Software Foundation (1.8) <br />
INFO 11:34:25 OS: macosx (10.16)<br />
INFO 11:34:25 Processor: x86-64<br />
<br />
</pre><br />
<br />
There are several ways of setting the heap size depending on how you run Protege. Note that for 64 bit windows machines there is a but in InstallAnywhere that prevents the user from setting the heap size over something like 1.5G. So in this case you will have to set up the run.bat script method of starting Protege.<br />
<br />
__TOC__<br />
<br />
<br />
==== Start Protege by Protege.exe/Protege or by double-cliking on the Protege icon (Windows/Linux) ====<br />
<br />
Michael DeBellis wrote on 2021/12/22:<br />
<br />
<start><br />
Needing more memory for Desktop Protege is a common issue and there is a simple solution. In the main directory where you have Protege [version 5.5 in 2021] there should be a file called Protege.I4J.ini That file is what Protege looks at when it starts up to determine how much memory Java can allocate. If you edit that file in Notepad or some other lightweight text processor it should currently look like this:<br />
<br />
-Xms200M<br />
-Xmx500M<br />
-Xss16M<br />
<br />
Xmx is the one you want to edit (I would recommend you make a copy of the original file first). That specifies the maximum amount of memory Protege can use. Xms is the initial memory that will be allocated and Xss defines the increments used when allocating more memory. The main thing to keep in mind is not to allocate so much memory that it starts to limit the performance of other programs which of course depends on how much memory your desktop or laptop have. <br />
<br />
<end><br />
<br />
For '''Protege 3.x''' you can do this in the Protege UI.<br />
* Go to '''File -> Preferences menu -> Protege.lax'''<br />
* Update the second column of the row containing <code>lax.nl.java.option.java.heap.size.max</code><br />
* Click on OK<br />
<br />
Please note that the changes take effect the next time you start Protege.<br />
<br />
Below is a screenshot of the Protege.lax panel.<br />
<br />
<br />
[[Image:Preferences-protege.lax.png]]<br />
<br />
<br />
For '''Protege 4''', you must edit directly the Protege.lax file in a text editor.<br />
<br />
Edit the following line in the Protege.lax file in the Protege installation directory:<br />
<br />
lax.nl.java.option.java.heap.size.max=100000000<br />
<br />
==== Start Protege by double-clicking on the Protege icon (Mac) ====<br />
<br />
If you run Protege on a Mac by double clicking an icon, you need to edit the Info.plist file that is hidden within that icon. Right click the icon (or ^-click for one button mouses) and click "show package contents". A new finder window will come up. Double click "Contents" and then "Info.plist". Traverse down the tree as follows: "Root" --> "Java" --> "JVMOptions". In JVMOptions edit the -Xmx line to indicate the correct memory usage. (Add the line <string>-Xmx2400M</string> if it's not there initially.)<br />
<key>JVMOptions</key><br />
<array><br />
<string>-Dapple.laf.useScreenMenuBar=true</string><br />
<string>-Xss16M</string><br />
<string>-Xms500M</string><br />
<string>-Xmx1400M</string><br />
<br />
<br />
==== Start Protege by double-clicking on the applescript file (Mac) ====<br />
<br />
If you run Protege on a Mac by double clicking the applescript file then you need to modify the -Xmx line in the script.<br />
<br />
<br />
==== Start Protege from the command line ====<br />
<br />
To run Protege from the command line, write in a terminal:<br />
<br />
.\run.sh<br />
<br />
(or, if on Windows, <code>run.bat</code>). You may change the heap size by editing the run script in a text editor, and change the value of the <code>-Xmx</code> argument. For example, to start with a 500MB heap size, use <code>-Xmx500M</code>. Read more on setting the heap size as an argument for generic Java applications [https://docs.oracle.com/javase/8/docs/technotes/tools/windows/java.html here] and [http://docs.oracle.com/javase/8/docs/technotes/guides/vm/gctuning/index.html here].<br />
<br />
Note that on Windows machines if you have installed the version of Protege that comes with its own jvm, you may need to change the path to java to jre\bin\java.exe. So for instance, to get 2G of heap space, you might change the Protege 4.2 run.bat file to be:<br />
<br />
<code>jre\bin\java.exe -Xmx2G -Dlog4j.configuration=file:log4j.xml -DentityExpansionLimit=100000000 -Dfile.encoding=utf-8 -Dorg.protege.plugin.dir=plugins -classpath bin/felix.jar;bin/ProtegeLauncher.jar org.protege.osgi.framework.Launcher</code><br />
<br />
<br />
[[Category:Protege documentation]]</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Protege-OWL_4_FAQ&diff=13773Protege-OWL 4 FAQ2021-12-22T20:23:02Z<p>Samsontu: </p>
<hr />
<div>__TOC__<br /><br />
<br />
== Protege Desktop Frequently Asked Questions ==<br />
<br />
<span style="color:red; font-weight:bold;">This FAQ is specific to Protege Desktop, versions 4, 5 and above.</span><br />
<br />
If you're working with older versions of Protege, you might find the following alternative FAQs helpful:<br />
<br />
* [[Protege-OWL_3_FAQ|Protege-OWL 3.x FAQ]]<br />
* [http://protege.stanford.edu/doc/faq.html Protege-Frames FAQ]<br />
* [http://protege.stanford.edu/doc/file_encodings.html Protege file encoding FAQ]<br />
<br />
<br />
=== How do I install Protege Desktop? ===<br />
Protege Desktop is [http://protege.stanford.edu/products.php#desktop-protege available for download] from the main Protege website. If you're new to Protege, we ask that you read about the different installation options currently available to determine which best suits your needs:<br />
<br />
* '''InstallyAnywhere platform independent installer program''' - this is the recommended method of installation for beginners and also for users that want a "double-clickable" executable file. The primary reason we recommend this method for beginners is that Protege Desktop requires a 1.6 version of the Java Virtual Machine to be present. The installer makes it very easy for you to install the correct version of the Java VM - or - if you already have Java installed, you can indicate the location during the install process. The installer also provides an executable file that you can double-click to launch Protege Desktop, e.g., "Protege.exe" on Windows, etc.<br />
<br />
* '''ZIP file''' - we provide a ZIP file for more advanced users that are familiar with how to make sure the proper version of Java is present. This is also a convenient installation for users that do not require an executable file to launch Protege Desktop.<br />
<br />
* '''Application bundle file''' - this is a new offering in Protege 4.1 and above that we hope will be an improvement for OS X users.<br />
<br />
=== Where can I find user documentation for Protege Desktop? ===<br />
Please refer to the [[Protege4UserDocs#Protege-OWL_Editor|Protege documentation page]] on this wiki for a list of available documentation.<br />
<br />
=== Where do I ask questions and report bugs? ===<br />
Please post comments, questions, and bug reports on the [http://mailman.stanford.edu/mailman/listinfo/protege-user protege-user mailing list]. Note that you must be subscribed to the list in order to post messages. If you have difficulties subscribing or unsubscribing from protege-user, please contact the [mailto:protege-user-owner@lists.stanford.edu list owners].<br />
<br />
=== Where can I look at a list known bugs and feature requests? ===<br />
<br />
Visit our issue tracker on GitHub: https://github.com/protegeproject/protege/issues?state=open.<br />
<br />
=== Why do I get a message about a damaged installer file on the Mac? ===<br />
OS X users might see the following error message when trying to install Protege Desktop:<br />
<br />
<br />
[[Image:Mac_damaged_installer_error_msg.png]]<br />
<br />
<br />
This is a misleading error message from Apple's [http://support.apple.com/kb/ht5290 Gatekeeper] software. By default, Gatekeeper is configured to only allow download and installation of applications from the Mac App Store and identified developers. The Protege Desktop software does not yet carry "identified developer" status. To successfully install Protege Desktop, navigate to Apple menu | System Preferences… | Security & Privacy | General tab, and select "Anywhere" from "Allow applications downloaded from".<br />
<br />
=== Why am I getting "An error related to DOT has occurred" when trying to use the OWLViz plug-in? ===<br />
If you see this error when trying to use OWLViz, it means that you have not completed some of the necessary steps to configure this plug-in. Complete documentation for fixing this error is available in the [http://protegewiki.stanford.edu/index.php/OWLViz#Troubleshooting troubleshooting section] of the OWLViz documentation.<br />
<br />
=== How do I change the name of an entity (class, property, individual) in my ontology? ===<br />
Select the Refactor | Change entity URI... menu item. In the resulting Change entity URI dialog box, enter the new name in the text box, and click the OK button.<br />
<br />
=== Why does my ontology contain classes named Error1, Error2, ...? ===<br />
See the [[Protege4ErrorClasses|Error Classes]] page for a description of this new OWL API feature.<br />
<br />
=== How do I change the allocated heap memory when I get the Java out-of-memory error? ===<br />
See the [[Setting_Heap_Size]] page for instructions.<br />
<br />
=== How do I edit/use SWRL rules in Protege ===<br />
* Create a new tab (Window -> Views -> Create new tab...) called something like Rules, SWRL or whatever you prefer [OPTIONAL]<br />
* Select the Window -> Views -> Ontology views -> Rules menu and drop the "Rules" view in a tab (for example the one created in the previous step)<br />
* Different reasoners have different level of support for rules. Pellet has the best support for SWRL rules. If you don't see Pellet listed in your Reasoner menu, install it (Open Files -> Preferences, select Plugins tab, press on "Check for downloads now" button, select and install Pellet) <br />
* In the Reasoner menu select the the Pellet reasoner [IMPORTANT]<br />
* View/Create/Edit/Delete SWRL rules in the "Rules" view<br />
* Start (Reasoner -> Start reasoner) or synchronize (Reasoner -> Synchronize reasoner) the reasoner (you can also do it with CTRL+R or COMMAND+R on Mac)<br />
* See results of the execurted rules in you other views<br />
<br />
=== What are the pros and cons of DL Query, SPARQL (with OWL entailment regime), and SQWRL===<br />
A DL Query is a OWL class expression. It<br />
* Returns results that can be superclasses, subclasses, or individuals of the class expression.<br />
* Has compact notation<br />
* Cannot use variables, therefore cannot compare values from different properties e.g., (forall all individuals ?x of class C where ?x.length = ?x.width)<br />
* Has limited sets of operators (e.g., can use regular expressions on strings but cannot do arithmetic)<br />
* Uses open-world assumption<br />
* Resolves queries relative to import closure, does not support federated queries<br />
* Is supported by any OWL reasoning system (Protege has GUI for DL queries)<br />
<br />
SPARQL query is a graph pattern. It<br />
* Can match against anything against graph patterns.<br />
* Has a rich set of operators and functions on numbers, strings, date/time, and terms<br />
* Is widely supported (although not all SPARQL engine support OWL2 entailment regime)<br />
* Can be resolved against relational databases with mappings (e.g., Ontop)<br />
* Supports federated queries across the net<br />
* Can work with OWL ontology because of formalized OWL to RDF mapping. Complex class expressions have very verbose RDF representation.<br />
<br />
SQWRL is an extension of OWL/SWRL. It<br />
* Natively understands OWL<br />
* Allows you to query for individuals only<br />
* Has an extensible collection of built-ins (including the ability to do arithmetic)<br />
* Has set operators that “close the world”<br />
* Allows comparison of values of different properties on the same individual<br />
* Is supported by Protege only<br />
* Does not support federated queries across the net</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Setting_Heap_Size&diff=13772Setting Heap Size2021-12-22T19:40:47Z<p>Samsontu: </p>
<hr />
<div><span style="font-weight:bold;font-size:18px;">Setting the Heap Size</span><br />
<br />
<br />
<span style="font-weight:bold;font-size:16px;">Recommendations for setting the heap size (read first!)</span><br />
<br />
<br />
You must be careful about setting the heap size parameter. If you set it too low then you will get "out of memory" errors. If you set it too high then your system will hang or you will suffer poor performance because parts of the jvm will be swapped in and out of memory. A rule of thumb is that you should not set this parameter larger than about 80% of your free physical memory. On Windows XP machines you can determine your free physical memory from the Performance tab of the Task Manager application. On Mac machines, click the apple (upper left hand corner and "about this mac"). On Linux machines, you can use the wonderful proc filesystem and look at the meminfo "file".<br />
<br />
Boosting the heap size parameter will allow you to read in larger file-based projects. It will also improve the performance of the database back-end since more memory is available for caching.<br />
<br />
The most common source of very slow performance on older systems (or laptops) is having the heap size set too large. If your system does not have 100MB of free memory then even the Protege default value is too big and you should make it smaller (or buy more memory). <br />
<br />
The best way to know if you have succeeded in changing the memory settings is to look at the console when Protege starts up. Protege will print out the memory settings as they start. The console or the log during startup will look something like this:<br />
<pre><br />
INFO 11:34:25 ------------------------------------ Protege -----------------------------------<br />
INFO 11:34:25 Protege Desktop<br />
INFO 11:34:25 Version 5.5.0, Build <br />
INFO 11:34:25 <br />
INFO 11:34:25 <br />
INFO 11:34:25 ----------------------------------- Platform -----------------------------------<br />
INFO 11:34:25 Java: JVM 1.8.0_121-b13 Memory: 2237M<br />
INFO 11:34:25 Language: en, Country: US<br />
INFO 11:34:25 Framework: Apache Software Foundation (1.8) <br />
INFO 11:34:25 OS: macosx (10.16)<br />
INFO 11:34:25 Processor: x86-64<br />
<br />
</pre><br />
<br />
There are several ways of setting the heap size depending on how you run Protege. Note that for 64 bit windows machines there is a but in InstallAnywhere that prevents the user from setting the heap size over something like 1.5G. So in this case you will have to set up the run.bat script method of starting Protege.<br />
<br />
__TOC__<br />
<br />
<br />
==== Start Protege by Protege.exe/Protege or by double-cliking on the Protege icon (Windows/Linux) ====<br />
<br />
If you start Protege on a Windows/Linux machine by double clicking on the Protege.exe/Protege or the Protege icon, you need to update the Protege.lax file.<br />
<br />
By default the Protege.lax file specifies a heap of 100MB for Protege 3.x and 200MB for Protege 4.<br />
<br />
<br />
For '''Protege 3.x''' you can do this in the Protege UI.<br />
* Go to '''File -> Preferences menu -> Protege.lax'''<br />
* Update the second column of the row containing <code>lax.nl.java.option.java.heap.size.max</code><br />
* Click on OK<br />
<br />
Please note that the changes take effect the next time you start Protege.<br />
<br />
Below is a screenshot of the Protege.lax panel.<br />
<br />
<br />
[[Image:Preferences-protege.lax.png]]<br />
<br />
<br />
For '''Protege 4''', you must edit directly the Protege.lax file in a text editor.<br />
<br />
Edit the following line in the Protege.lax file in the Protege installation directory:<br />
<br />
lax.nl.java.option.java.heap.size.max=100000000<br />
<br />
==== Start Protege by double-clicking on the Protege icon (Mac) ====<br />
<br />
If you run Protege on a Mac by double clicking an icon, you need to edit the Info.plist file that is hidden within that icon. Right click the icon (or ^-click for one button mouses) and click "show package contents". A new finder window will come up. Double click "Contents" and then "Info.plist". Traverse down the tree as follows: "Root" --> "Java" --> "JVMOptions". In JVMOptions edit the -Xmx line to indicate the correct memory usage. (Add the line <string>-Xmx2400M</string> if it's not there initially.)<br />
<key>JVMOptions</key><br />
<array><br />
<string>-Dapple.laf.useScreenMenuBar=true</string><br />
<string>-Xss16M</string><br />
<string>-Xms500M</string><br />
<string>-Xmx1400M</string><br />
<br />
<br />
==== Start Protege by double-clicking on the applescript file (Mac) ====<br />
<br />
If you run Protege on a Mac by double clicking the applescript file then you need to modify the -Xmx line in the script.<br />
<br />
<br />
==== Start Protege from the command line ====<br />
<br />
To run Protege from the command line, write in a terminal:<br />
<br />
.\run.sh<br />
<br />
(or, if on Windows, <code>run.bat</code>). You may change the heap size by editing the run script in a text editor, and change the value of the <code>-Xmx</code> argument. For example, to start with a 500MB heap size, use <code>-Xmx500M</code>. Read more on setting the heap size as an argument for generic Java applications [https://docs.oracle.com/javase/8/docs/technotes/tools/windows/java.html here] and [http://docs.oracle.com/javase/8/docs/technotes/guides/vm/gctuning/index.html here].<br />
<br />
Note that on Windows machines if you have installed the version of Protege that comes with its own jvm, you may need to change the path to java to jre\bin\java.exe. So for instance, to get 2G of heap space, you might change the Protege 4.2 run.bat file to be:<br />
<br />
<code>jre\bin\java.exe -Xmx2G -Dlog4j.configuration=file:log4j.xml -DentityExpansionLimit=100000000 -Dfile.encoding=utf-8 -Dorg.protege.plugin.dir=plugins -classpath bin/felix.jar;bin/ProtegeLauncher.jar org.protege.osgi.framework.Launcher</code><br />
<br />
<br />
[[Category:Protege documentation]]</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=OntoViz&diff=13639OntoViz2017-07-19T15:51:11Z<p>Samsontu: /* Mac specific notes on installation */</p>
<hr />
<div>{{Plugin<br />
|Description=The OntoViz Tab allows you to visualize Protege ontologies with AT&T's highly sophisticated Graphviz visualization software.<br />
|PluginType=Tab Widget<br />
|ForApplication1=Protege-Frames<br />
|ForApplication2=Protege-OWL<br />
|ForApplication3=Protege Client-Server<br />
|Screenshot=OntoViz.gif<br />
|HomepageURL=http://protegewiki.stanford.edu/index.php/OntoViz<br />
|DeveloperID1=Michael Sintek<br />
|LastUpdated=July 11, 2007<br />
|Topic1=Visualization<br />
|License=Mozilla Public License.<br />
|Affiliation1=Stanford University<br />
|Affiliation2=German Research Center for Artificial Intelligence<br />
}}<br />
<div style="float:left;"><br />
__TOC__<br />
<br />
== Detailed Description ==<br />
The OntoViz Tab allows you to visualize Protege ontologies with the help of a highly sophisticated graph visualization software called [http://www.graphviz.org/ Graphviz] from AT&T. The types of visualizations are highly configurable and include:<br />
* Picking a set of classes or instances to visualize part of an ontology<br />
* Displaying slots and slot edges<br />
* Specifying colors for nodes and edges.<br />
* When picking only a few classes or instances, you can apply various closure operators (e.g., subclasses, superclasses) to visualize their vicinity.<br />
<br />
<br />
== Installation ==<br />
The OntoViz Tab is bundled with the [http://protege.stanford.edu/download/download.html "full" installation of Protege] (please use version 3.3.1 or 3.4.* or 3.5).<br />
<br />
Once you have installed Protege, you must also:<br />
<br />
a). Install the appropriate version of the [http://www.graphviz.org/ Graphviz] graph visualization software for your platform. (Graphviz 2.30 or later does not work with Ontoviz. Graphviz 2.14 does work.)<br />
<br />
b). Modify your "protege.properties" file to specify where you installed Graphviz. For example, if you installed Graphviz in C:\Program Files\ATT\Graphviz\, you would add the following line to protege.properties:<br />
<br />
<code>dot.command=C\:\\Program\ Files\\ATT\Graphviz\\bin\\dot</code><br />
<br />
NOTE: you may need to modify your file structure to match the path in your [[protege.properties]] file. Check [[here|protege.properties]] for more details.<br />
<br />
The protege.properties file is located in the root directory of your Protege installation and an example protege.properties file is included in the OntoViz subdirectory for your reference <br />
<br />
<code><protege-install-dir>/plugins/dfki.protege.ontoviz/protege.properties</code><br />
<br />
In addition to specifying the path to the Graphviz dot executable, you can set the following optional attributes:<br />
<br />
<pre>dot.font=<font-name> (optional; usually Arial)<br />
<br />
dot.fontsize=<size-specification> (optional; usually -2 or -3)<br />
<br />
dot.fontpath=<path-to-ttf-directory> (needed on some flavors of Unix; on Solaris: /usr/openwin/lib/X11/fonts/TrueType)</pre><br />
<br />
===Mac specific notes on installation===<br />
<br />
Many thanks go to Andy Spydell for providing the following Macintosh specific instructions for configuring OntoViz and Graphviz. Andy used Mac OS X (10.4):<br />
<br />
Download the Mac OS X version of Graphviz.... I chose the disk image version (dmg) version. Upon extracting and mounting, you will find two files contained within the disk image: Graphviz (an Application) and an Examples directory. [Graphviz 2.30 or later is known to be incompatible with Ontoviz. Graphviz 2.14 does work. Versions between 2.14 and 2.30 have not been tested.]<br />
<br />
Create a directory to hold the Graphviz application and Examples directory at a location of your choice (for example, I created a directory called /Users/andy/Developer/Tools/Graphviz). The disk image is named something like "Graphviz 1.13 (v16)", which makes a poor directory name due to the spaces, period, and parentheses.<br />
<br />
Copy the Graphviz application and Examples directory into your newly created directory.<br />
<br />
In the Finder, locate the file named "protege.properties" in the Protege directory, and open it with TextEdit (right-click, open, other, select TextEdit). You need to add a line to the file that tells Protege where to find the Graphviz UNIX executable. For me, the line of text looks exactly like:<br />
<br />
<code>dot.command=/Users/andy/Developer/Tools/Graphviz/Graphviz.app/Contents/MacOS/dot</code><br />
<br />
Save and close TextEdit.<br />
<br />
<div style="border: 1px solid pink; padding: 3px;">''Comment from another Mac user:'' these instructions did not work for me. I added the following property to the protege.properties Property Table (accessible from the File | Preferences... | Property Files tab):<br />
<br />
Property = OWLViz.Dot.Path, Value = full path name of location of dot executable<br />
<br />
Then it worked for me.</div><br />
<br />
If you don't see any graphs after you begin using the OntoViz Tab in Protege, verify that the dot.command value does in fact represent the "dot" UNIX executable. The easiest way to do this is with the Terminal and "ls" command. Copy the dot.command value from the protege.properties file and paste it into a Terminal window:<br />
<br />
<code>terminal> ls /Users/andy/Developer/Tools/Graphviz/Graphviz.app/Contents/MacOS/dot</code><br />
<br />
If the file is not found, you will then need to correct the path value in protege.properties.<br />
<br />
== Documentation ==<br />
<br />
To enable the OntoViz Tab in Protege, choose the menu item Project -> Configure, check the checkbox next to the entry for the OntoViz tab widget, and click OK.<br />
<br />
[[Image:Configure-ontoviz.jpg|none]]<br />
<br />
<br />
=== Creating a graph ===<br />
<br />
To create a graph, select a class from your ontology in the Classes pane, click the "add class" button in the upper left "Config" area of the tab, check several of the options such as "sub", "sup", "slx", and click the "Create Graph" button. The same process can be used for creating graphs of instances by using the "add instance" instead of the "add class" button. To remove an entry from the Config table, use the "remove class" button.<br />
<br />
[[Image:Ontoviz-create-graph.jpg|none]]<br />
<br />
<br />
Selecting a node in the graph displays the corresponding class in the classes tree (and vice versa):<br />
<br />
[[Image:Ontoviz-select-class-in-graph.jpg]]<br />
<br />
<br />
You can also use the middle and right mouse buttons for zooming:<br />
<br />
[[Image:Ontoviz-zoom-in-on-graph.jpg]]<br />
<br />
<br />
=== Fine tuning your graph ===<br />
<br />
To fine tune your graph, e.g., for showing only a part of your ontology, the following options are available:<br />
<br />
'''1. Options per class/instance, i.e., per row in the Config table.'''<br />
<br />
Check or uncheck any of the following check boxes next to an entry in the Config table:<br />
* sub - subclass closure<br />
* sup - superclass closure<br />
* slx - slot extension<br />
* isx - inverse slot extension<br />
* slt - slots<br />
* sle - slot edges<br />
* ins - instances<br />
* sys - system frames<br />
<br />
The (simplified) semantics for each row in the table are as follows: <br />
<br />
<code>closure := {frame[row]}</code><br />
<br />
* '''sub/sup:''' compute the subclass and superclass closures if frame is a class (independently; otherwise we would always end up with all classes):<br /><code>closure := closure U subClosure U supClosure</code><br />
* '''slx/isx:''' for all classes/instances in closure, find the classes/instances that are reachable by a slot of type INSTANCE or CLASS (the maximum depth can be configured on the global options window; default is 1 for classes and 3 for instances):<br /><code>closure := closure U slotExtension</code><br />
* '''ins:''' add all instances of classes in closure to closure:<br /><code>closure = closure U instances(closure)</code><br />
* '''slt/sle/sys:''' (globally) mark all frames in closure accordingly<br />
<br />
''If sys is not true, in all steps above ignore system classes and slots.''<br />
<br />
It is also possible to add a class more than once to the Config table with a different options set. Some examples using the newspaper project might be:<br />
<br />
a. Inspect one class in the middle of the ontology, e.g., Employee.<br />
<br />
<pre><br />
Employee sup slt sys<br />
Employee sub<br />
<br />
shows all superclasses of Employee WITH template slots and all subclasses WITHOUT template slots</pre><br />
<br />
[[Image:Ontoviz-inspect-multiple.jpg]]<br />
<br />
<br />
b. Show a class and its "template slot neighborhood", e.g., Newspaper.<br />
<br />
<pre>Newspaper sup slx isx sys</pre><br />
<br />
<br />
'''2. Options for slots'''<br />
<br />
Slots can be configured individually by pressing the colored "S" button. A slot can be configured as "default", "hidden", or "configured" (at the moment, a configured slot means that the user selected color and preferred arrow direction). Furthermore, all "default" slots can be hidden ("hide slots as default" check box). To configure a slot, click on the "default" cell in the table.<br />
<br />
[[Image:Ontoviz-configure-slots.jpg]]<br />
<br />
<br />
'''3. Global options'''<br />
<br />
The following global options are available in the "Ontoviz Global Options" dialog by clicking on the "Op" button.<br />
<br />
* save as gif - save the graph as a GIF image in the directory where the project resides, or in the main Protege directory, if the project has not yet been saved<br />
* show io :STANDARD-CLASS edges - if this box is checked, instances of ("io") :STANDARD-CLASS links are shown (results in really huge graphs!)<br />
* show system own slots - if this box is checked, system own slots are shown (e.g., :NAME), which are not very useful except for debugging system stuff<br />
* slot edges dashed - use dashed lines for slot edges (useful for printing)<br />
* show instances only - don't show the classes (useful if you want to inspect complex relationships between many instances)<br />
* on the colors tab, you can configure colors for nodes and edges.<br />
<br />
<br />
[[Image:Global-options.jpg]] [[Image:Global-options2.jpg]]<br />
<br />
<br />
== Screenshots ==<br />
<br />
To follow are some additional screenshots of the OntoViz Tab. The graphs were generated using the newspaper example project that comes with all installations of Protege. Please note that these screenshots were created using an older version of Protege.<br />
<br />
<br />
[[Image:Ontoviz-simple.gif]]<br />
<br />
<br />
[[Image:Ontoviz-slot-edges.gif]]<br />
<br />
<br />
[[Image:Ontoviz-template-slots.gif]]<br />
<br />
<br />
[[Image:Ontoviz-rdf.gif]]<br />
<br />
<br />
[[Image:Ontoviz-metaclasses.gif]]<br />
<br />
<br />
[[Image:Ontoviz-ont-plus-instances.gif]]<br />
<br />
<br />
<br />
== Level of Support ==<br />
Unsupported. The source code for this tab is available in the Protege Subversion repository. To view the code, please use this URL:<br />
<br />
http://smi-protege.stanford.edu/svn/ontoviz-tab/trunk/<br />
<br />
... or, to check out the code, you may use this URL:<br />
<br />
http://smi-protege.stanford.edu/repos/protege/ontoviz-tab/trunk/<br />
<br />
If you have questions about OntoViz, you can try posting them on the [http://mailman.stanford.edu/mailman/listinfo/protege-discussion protege-discussion mailing list] and someone from the Protege community may be able to help you.<br />
<br /><br /><br />
</div></div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=OntoViz&diff=13638OntoViz2017-07-19T15:47:54Z<p>Samsontu: /* Installation */</p>
<hr />
<div>{{Plugin<br />
|Description=The OntoViz Tab allows you to visualize Protege ontologies with AT&T's highly sophisticated Graphviz visualization software.<br />
|PluginType=Tab Widget<br />
|ForApplication1=Protege-Frames<br />
|ForApplication2=Protege-OWL<br />
|ForApplication3=Protege Client-Server<br />
|Screenshot=OntoViz.gif<br />
|HomepageURL=http://protegewiki.stanford.edu/index.php/OntoViz<br />
|DeveloperID1=Michael Sintek<br />
|LastUpdated=July 11, 2007<br />
|Topic1=Visualization<br />
|License=Mozilla Public License.<br />
|Affiliation1=Stanford University<br />
|Affiliation2=German Research Center for Artificial Intelligence<br />
}}<br />
<div style="float:left;"><br />
__TOC__<br />
<br />
== Detailed Description ==<br />
The OntoViz Tab allows you to visualize Protege ontologies with the help of a highly sophisticated graph visualization software called [http://www.graphviz.org/ Graphviz] from AT&T. The types of visualizations are highly configurable and include:<br />
* Picking a set of classes or instances to visualize part of an ontology<br />
* Displaying slots and slot edges<br />
* Specifying colors for nodes and edges.<br />
* When picking only a few classes or instances, you can apply various closure operators (e.g., subclasses, superclasses) to visualize their vicinity.<br />
<br />
<br />
== Installation ==<br />
The OntoViz Tab is bundled with the [http://protege.stanford.edu/download/download.html "full" installation of Protege] (please use version 3.3.1 or 3.4.* or 3.5).<br />
<br />
Once you have installed Protege, you must also:<br />
<br />
a). Install the appropriate version of the [http://www.graphviz.org/ Graphviz] graph visualization software for your platform. (Graphviz 2.30 or later does not work with Ontoviz. Graphviz 2.14 does work.)<br />
<br />
b). Modify your "protege.properties" file to specify where you installed Graphviz. For example, if you installed Graphviz in C:\Program Files\ATT\Graphviz\, you would add the following line to protege.properties:<br />
<br />
<code>dot.command=C\:\\Program\ Files\\ATT\Graphviz\\bin\\dot</code><br />
<br />
NOTE: you may need to modify your file structure to match the path in your [[protege.properties]] file. Check [[here|protege.properties]] for more details.<br />
<br />
The protege.properties file is located in the root directory of your Protege installation and an example protege.properties file is included in the OntoViz subdirectory for your reference <br />
<br />
<code><protege-install-dir>/plugins/dfki.protege.ontoviz/protege.properties</code><br />
<br />
In addition to specifying the path to the Graphviz dot executable, you can set the following optional attributes:<br />
<br />
<pre>dot.font=<font-name> (optional; usually Arial)<br />
<br />
dot.fontsize=<size-specification> (optional; usually -2 or -3)<br />
<br />
dot.fontpath=<path-to-ttf-directory> (needed on some flavors of Unix; on Solaris: /usr/openwin/lib/X11/fonts/TrueType)</pre><br />
<br />
===Mac specific notes on installation===<br />
<br />
Many thanks go to Andy Spydell for providing the following Macintosh specific instructions for configuring OntoViz and Graphviz. Andy used Mac OS X (10.4):<br />
<br />
Download the latest [http://www.pixelglow.com/graphviz/download/ Mac OS X version of Graphviz] (current is 1.13 v16). I chose the disk image version (dmg) version. Upon extracting and mounting, you will find two files contained within the disk image: Graphviz (an Application) and an Examples directory.<br />
<br />
Create a directory to hold the Graphviz application and Examples directory at a location of your choice (for example, I created a directory called /Users/andy/Developer/Tools/Graphviz). The disk image is named something like "Graphviz 1.13 (v16)", which makes a poor directory name due to the spaces, period, and parentheses.<br />
<br />
Copy the Graphviz application and Examples directory into your newly created directory.<br />
<br />
In the Finder, locate the file named "protege.properties" in the Protege directory, and open it with TextEdit (right-click, open, other, select TextEdit). You need to add a line to the file that tells Protege where to find the Graphviz UNIX executable. For me, the line of text looks exactly like:<br />
<br />
<code>dot.command=/Users/andy/Developer/Tools/Graphviz/Graphviz.app/Contents/MacOS/dot</code><br />
<br />
Save and close TextEdit.<br />
<br />
<div style="border: 1px solid pink; padding: 3px;">''Comment from another Mac user:'' these instructions did not work for me. I added the following property to the protege.properties Property Table (accessible from the File | Preferences... | Property Files tab):<br />
<br />
Property = OWLViz.Dot.Path, Value = full path name of location of dot executable<br />
<br />
Then it worked for me.</div><br />
<br />
If you don't see any graphs after you begin using the OntoViz Tab in Protege, verify that the dot.command value does in fact represent the "dot" UNIX executable. The easiest way to do this is with the Terminal and "ls" command. Copy the dot.command value from the protege.properties file and paste it into a Terminal window:<br />
<br />
<code>terminal> ls /Users/andy/Developer/Tools/Graphviz/Graphviz.app/Contents/MacOS/dot</code><br />
<br />
If the file is not found, you will then need to correct the path value in protege.properties.<br />
<br />
== Documentation ==<br />
<br />
To enable the OntoViz Tab in Protege, choose the menu item Project -> Configure, check the checkbox next to the entry for the OntoViz tab widget, and click OK.<br />
<br />
[[Image:Configure-ontoviz.jpg|none]]<br />
<br />
<br />
=== Creating a graph ===<br />
<br />
To create a graph, select a class from your ontology in the Classes pane, click the "add class" button in the upper left "Config" area of the tab, check several of the options such as "sub", "sup", "slx", and click the "Create Graph" button. The same process can be used for creating graphs of instances by using the "add instance" instead of the "add class" button. To remove an entry from the Config table, use the "remove class" button.<br />
<br />
[[Image:Ontoviz-create-graph.jpg|none]]<br />
<br />
<br />
Selecting a node in the graph displays the corresponding class in the classes tree (and vice versa):<br />
<br />
[[Image:Ontoviz-select-class-in-graph.jpg]]<br />
<br />
<br />
You can also use the middle and right mouse buttons for zooming:<br />
<br />
[[Image:Ontoviz-zoom-in-on-graph.jpg]]<br />
<br />
<br />
=== Fine tuning your graph ===<br />
<br />
To fine tune your graph, e.g., for showing only a part of your ontology, the following options are available:<br />
<br />
'''1. Options per class/instance, i.e., per row in the Config table.'''<br />
<br />
Check or uncheck any of the following check boxes next to an entry in the Config table:<br />
* sub - subclass closure<br />
* sup - superclass closure<br />
* slx - slot extension<br />
* isx - inverse slot extension<br />
* slt - slots<br />
* sle - slot edges<br />
* ins - instances<br />
* sys - system frames<br />
<br />
The (simplified) semantics for each row in the table are as follows: <br />
<br />
<code>closure := {frame[row]}</code><br />
<br />
* '''sub/sup:''' compute the subclass and superclass closures if frame is a class (independently; otherwise we would always end up with all classes):<br /><code>closure := closure U subClosure U supClosure</code><br />
* '''slx/isx:''' for all classes/instances in closure, find the classes/instances that are reachable by a slot of type INSTANCE or CLASS (the maximum depth can be configured on the global options window; default is 1 for classes and 3 for instances):<br /><code>closure := closure U slotExtension</code><br />
* '''ins:''' add all instances of classes in closure to closure:<br /><code>closure = closure U instances(closure)</code><br />
* '''slt/sle/sys:''' (globally) mark all frames in closure accordingly<br />
<br />
''If sys is not true, in all steps above ignore system classes and slots.''<br />
<br />
It is also possible to add a class more than once to the Config table with a different options set. Some examples using the newspaper project might be:<br />
<br />
a. Inspect one class in the middle of the ontology, e.g., Employee.<br />
<br />
<pre><br />
Employee sup slt sys<br />
Employee sub<br />
<br />
shows all superclasses of Employee WITH template slots and all subclasses WITHOUT template slots</pre><br />
<br />
[[Image:Ontoviz-inspect-multiple.jpg]]<br />
<br />
<br />
b. Show a class and its "template slot neighborhood", e.g., Newspaper.<br />
<br />
<pre>Newspaper sup slx isx sys</pre><br />
<br />
<br />
'''2. Options for slots'''<br />
<br />
Slots can be configured individually by pressing the colored "S" button. A slot can be configured as "default", "hidden", or "configured" (at the moment, a configured slot means that the user selected color and preferred arrow direction). Furthermore, all "default" slots can be hidden ("hide slots as default" check box). To configure a slot, click on the "default" cell in the table.<br />
<br />
[[Image:Ontoviz-configure-slots.jpg]]<br />
<br />
<br />
'''3. Global options'''<br />
<br />
The following global options are available in the "Ontoviz Global Options" dialog by clicking on the "Op" button.<br />
<br />
* save as gif - save the graph as a GIF image in the directory where the project resides, or in the main Protege directory, if the project has not yet been saved<br />
* show io :STANDARD-CLASS edges - if this box is checked, instances of ("io") :STANDARD-CLASS links are shown (results in really huge graphs!)<br />
* show system own slots - if this box is checked, system own slots are shown (e.g., :NAME), which are not very useful except for debugging system stuff<br />
* slot edges dashed - use dashed lines for slot edges (useful for printing)<br />
* show instances only - don't show the classes (useful if you want to inspect complex relationships between many instances)<br />
* on the colors tab, you can configure colors for nodes and edges.<br />
<br />
<br />
[[Image:Global-options.jpg]] [[Image:Global-options2.jpg]]<br />
<br />
<br />
== Screenshots ==<br />
<br />
To follow are some additional screenshots of the OntoViz Tab. The graphs were generated using the newspaper example project that comes with all installations of Protege. Please note that these screenshots were created using an older version of Protege.<br />
<br />
<br />
[[Image:Ontoviz-simple.gif]]<br />
<br />
<br />
[[Image:Ontoviz-slot-edges.gif]]<br />
<br />
<br />
[[Image:Ontoviz-template-slots.gif]]<br />
<br />
<br />
[[Image:Ontoviz-rdf.gif]]<br />
<br />
<br />
[[Image:Ontoviz-metaclasses.gif]]<br />
<br />
<br />
[[Image:Ontoviz-ont-plus-instances.gif]]<br />
<br />
<br />
<br />
== Level of Support ==<br />
Unsupported. The source code for this tab is available in the Protege Subversion repository. To view the code, please use this URL:<br />
<br />
http://smi-protege.stanford.edu/svn/ontoviz-tab/trunk/<br />
<br />
... or, to check out the code, you may use this URL:<br />
<br />
http://smi-protege.stanford.edu/repos/protege/ontoviz-tab/trunk/<br />
<br />
If you have questions about OntoViz, you can try posting them on the [http://mailman.stanford.edu/mailman/listinfo/protege-discussion protege-discussion mailing list] and someone from the Protege community may be able to help you.<br />
<br /><br /><br />
</div></div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Protege-OWL_4_FAQ&diff=13534Protege-OWL 4 FAQ2016-08-17T21:18:21Z<p>Samsontu: </p>
<hr />
<div>__TOC__<br /><br />
<br />
== Protege Desktop Frequently Asked Questions ==<br />
<br />
<span style="color:red; font-weight:bold;">This FAQ is specific to Protege Desktop, versions 4, 5 and above.</span><br />
<br />
If you're working with older versions of Protege, you might find the following alternative FAQs helpful:<br />
<br />
* [[Protege-OWL_3_FAQ|Protege-OWL 3.x FAQ]]<br />
* [http://protege.stanford.edu/doc/faq.html Protege-Frames FAQ]<br />
* [http://protege.stanford.edu/doc/file_encodings.html Protege file encoding FAQ]<br />
<br />
<br />
=== How do I install Protege Desktop? ===<br />
Protege Desktop is [http://protege.stanford.edu/products.php#desktop-protege available for download] from the main Protege website. If you're new to Protege, we ask that you read about the different installation options currently available to determine which best suits your needs:<br />
<br />
* '''InstallyAnywhere platform independent installer program''' - this is the recommended method of installation for beginners and also for users that want a "double-clickable" executable file. The primary reason we recommend this method for beginners is that Protege Desktop requires a 1.6 version of the Java Virtual Machine to be present. The installer makes it very easy for you to install the correct version of the Java VM - or - if you already have Java installed, you can indicate the location during the install process. The installer also provides an executable file that you can double-click to launch Protege Desktop, e.g., "Protege.exe" on Windows, etc.<br />
<br />
* '''ZIP file''' - we provide a ZIP file for more advanced users that are familiar with how to make sure the proper version of Java is present. This is also a convenient installation for users that do not require an executable file to launch Protege Desktop.<br />
<br />
* '''Application bundle file''' - this is a new offering in Protege 4.1 and above that we hope will be an improvement for OS X users.<br />
<br />
=== Where can I find user documentation for Protege Desktop? ===<br />
Please refer to the [[Protege4UserDocs#Protege-OWL_Editor|Protege documentation page]] on this wiki for a list of available documentation.<br />
<br />
=== Where do I ask questions and report bugs? ===<br />
Please post comments, questions, and bug reports on the [http://mailman.stanford.edu/mailman/listinfo/protege-user protege-user mailing list]. Note that you must be subscribed to the list in order to post messages. If you have difficulties subscribing or unsubscribing from protege-user, please contact the [mailto:protege-user-owner@lists.stanford.edu list owners].<br />
<br />
=== Where can I look at a list known bugs and feature requests? ===<br />
<br />
Visit our issue tracker on GitHub: https://github.com/protegeproject/protege/issues?state=open.<br />
<br />
=== Why do I get a message about a damaged installer file on the Mac? ===<br />
OS X users might see the following error message when trying to install Protege Desktop:<br />
<br />
<br />
[[Image:Mac_damaged_installer_error_msg.png]]<br />
<br />
<br />
This is a misleading error message from Apple's [http://support.apple.com/kb/ht5290 Gatekeeper] software. By default, Gatekeeper is configured to only allow download and installation of applications from the Mac App Store and identified developers. The Protege Desktop software does not yet carry "identified developer" status. To successfully install Protege Desktop, navigate to Apple menu | System Preferences… | Security & Privacy | General tab, and select "Anywhere" from "Allow applications downloaded from".<br />
<br />
=== Why am I getting "An error related to DOT has occurred" when trying to use the OWLViz plug-in? ===<br />
If you see this error when trying to use OWLViz, it means that you have not completed some of the necessary steps to configure this plug-in. Complete documentation for fixing this error is available in the [http://protegewiki.stanford.edu/index.php/OWLViz#Troubleshooting troubleshooting section] of the OWLViz documentation.<br />
<br />
=== How do I change the name of an entity (class, property, individual) in my ontology? ===<br />
Select the Refactor | Change entity URI... menu item. In the resulting Change entity URI dialog box, enter the new name in the text box, and click the OK button.<br />
<br />
=== Why does my ontology contain classes named Error1, Error2, ...? ===<br />
See the [[Protege4ErrorClasses|Error Classes]] page for a description of this new OWL API feature.<br />
<br />
=== How do I edit/use SWRL rules in Protege ===<br />
* Create a new tab (Window -> Views -> Create new tab...) called something like Rules, SWRL or whatever you prefer [OPTIONAL]<br />
* Select the Window -> Views -> Ontology views -> Rules menu and drop the "Rules" view in a tab (for example the one created in the previous step)<br />
* Different reasoners have different level of support for rules. Pellet has the best support for SWRL rules. If you don't see Pellet listed in your Reasoner menu, install it (Open Files -> Preferences, select Plugins tab, press on "Check for downloads now" button, select and install Pellet) <br />
* In the Reasoner menu select the the Pellet reasoner [IMPORTANT]<br />
* View/Create/Edit/Delete SWRL rules in the "Rules" view<br />
* Start (Reasoner -> Start reasoner) or synchronize (Reasoner -> Synchronize reasoner) the reasoner (you can also do it with CTRL+R or COMMAND+R on Mac)<br />
* See results of the execurted rules in you other views<br />
<br />
=== What are the pros and cons of DL Query, SPARQL (with OWL entailment regime), and SQWRL===<br />
A DL Query is a OWL class expression. It<br />
* Returns results that can be superclasses, subclasses, or individuals of the class expression.<br />
* Has compact notation<br />
* Cannot use variables, therefore cannot compare values from different properties e.g., (forall all individuals ?x of class C where ?x.length = ?x.width)<br />
* Has limited sets of operators (e.g., can use regular expressions on strings but cannot do arithmetic)<br />
* Uses open-world assumption<br />
* Resolves queries relative to import closure, does not support federated queries<br />
* Is supported by any OWL reasoning system (Protege has GUI for DL queries)<br />
<br />
SPARQL query is a graph pattern. It<br />
* Can match against anything against graph patterns.<br />
* Has a rich set of operators and functions on numbers, strings, date/time, and terms<br />
* Is widely supported (although not all SPARQL engine support OWL2 entailment regime)<br />
* Can be resolved against relational databases with mappings (e.g., Ontop)<br />
* Supports federated queries across the net<br />
* Can work with OWL ontology because of formalized OWL to RDF mapping. Complex class expressions have very verbose RDF representation.<br />
<br />
SQWRL is an extension of OWL/SWRL. It<br />
* Natively understands OWL<br />
* Allows you to query for individuals only<br />
* Has an extensible collection of built-ins (including the ability to do arithmetic)<br />
* Has set operators that “close the world”<br />
* Allows comparison of values of different properties on the same individual<br />
* Is supported by Protege only<br />
* Does not support federated queries across the net</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Protege-OWL_4_FAQ&diff=13533Protege-OWL 4 FAQ2016-08-17T21:17:41Z<p>Samsontu: </p>
<hr />
<div>__TOC__<br /><br />
<br />
== Protege Desktop Frequently Asked Questions ==<br />
<br />
<span style="color:red; font-weight:bold;">This FAQ is specific to Protege Desktop, versions 4, 5 and above.</span><br />
<br />
If you're working with older versions of Protege, you might find the following alternative FAQs helpful:<br />
<br />
* [[Protege-OWL_3_FAQ|Protege-OWL 3.x FAQ]]<br />
* [http://protege.stanford.edu/doc/faq.html Protege-Frames FAQ]<br />
* [http://protege.stanford.edu/doc/file_encodings.html Protege file encoding FAQ]<br />
<br />
<br />
=== How do I install Protege Desktop? ===<br />
Protege Desktop is [http://protege.stanford.edu/products.php#desktop-protege available for download] from the main Protege website. If you're new to Protege, we ask that you read about the different installation options currently available to determine which best suits your needs:<br />
<br />
* '''InstallyAnywhere platform independent installer program''' - this is the recommended method of installation for beginners and also for users that want a "double-clickable" executable file. The primary reason we recommend this method for beginners is that Protege Desktop requires a 1.6 version of the Java Virtual Machine to be present. The installer makes it very easy for you to install the correct version of the Java VM - or - if you already have Java installed, you can indicate the location during the install process. The installer also provides an executable file that you can double-click to launch Protege Desktop, e.g., "Protege.exe" on Windows, etc.<br />
<br />
* '''ZIP file''' - we provide a ZIP file for more advanced users that are familiar with how to make sure the proper version of Java is present. This is also a convenient installation for users that do not require an executable file to launch Protege Desktop.<br />
<br />
* '''Application bundle file''' - this is a new offering in Protege 4.1 and above that we hope will be an improvement for OS X users.<br />
<br />
=== Where can I find user documentation for Protege Desktop? ===<br />
Please refer to the [[Protege4UserDocs#Protege-OWL_Editor|Protege documentation page]] on this wiki for a list of available documentation.<br />
<br />
=== Where do I ask questions and report bugs? ===<br />
Please post comments, questions, and bug reports on the [http://mailman.stanford.edu/mailman/listinfo/protege-user protege-user mailing list]. Note that you must be subscribed to the list in order to post messages. If you have difficulties subscribing or unsubscribing from protege-user, please contact the [mailto:protege-user-owner@lists.stanford.edu list owners].<br />
<br />
=== Where can I look at a list known bugs and feature requests? ===<br />
<br />
Visit our issue tracker on GitHub: https://github.com/protegeproject/protege/issues?state=open.<br />
<br />
=== Why do I get a message about a damaged installer file on the Mac? ===<br />
OS X users might see the following error message when trying to install Protege Desktop:<br />
<br />
<br />
[[Image:Mac_damaged_installer_error_msg.png]]<br />
<br />
<br />
This is a misleading error message from Apple's [http://support.apple.com/kb/ht5290 Gatekeeper] software. By default, Gatekeeper is configured to only allow download and installation of applications from the Mac App Store and identified developers. The Protege Desktop software does not yet carry "identified developer" status. To successfully install Protege Desktop, navigate to Apple menu | System Preferences… | Security & Privacy | General tab, and select "Anywhere" from "Allow applications downloaded from".<br />
<br />
=== Why am I getting "An error related to DOT has occurred" when trying to use the OWLViz plug-in? ===<br />
If you see this error when trying to use OWLViz, it means that you have not completed some of the necessary steps to configure this plug-in. Complete documentation for fixing this error is available in the [http://protegewiki.stanford.edu/index.php/OWLViz#Troubleshooting troubleshooting section] of the OWLViz documentation.<br />
<br />
=== How do I change the name of an entity (class, property, individual) in my ontology? ===<br />
Select the Refactor | Change entity URI... menu item. In the resulting Change entity URI dialog box, enter the new name in the text box, and click the OK button.<br />
<br />
=== Why does my ontology contain classes named Error1, Error2, ...? ===<br />
See the [[Protege4ErrorClasses|Error Classes]] page for a description of this new OWL API feature.<br />
<br />
=== How do I edit/use SWRL rules in Protege ===<br />
* Create a new tab (Window -> Views -> Create new tab...) called something like Rules, SWRL or whatever you prefer [OPTIONAL]<br />
* Select the Window -> Views -> Ontology views -> Rules menu and drop the "Rules" view in a tab (for example the one created in the previous step)<br />
* Different reasoners have different level of support for rules. Pellet has the best support for SWRL rules. If you don't see Pellet listed in your Reasoner menu, install it (Open Files -> Preferences, select Plugins tab, press on "Check for downloads now" button, select and install Pellet) <br />
* In the Reasoner menu select the the Pellet reasoner [IMPORTANT]<br />
* View/Create/Edit/Delete SWRL rules in the "Rules" view<br />
* Start (Reasoner -> Start reasoner) or synchronize (Reasoner -> Synchronize reasoner) the reasoner (you can also do it with CTRL+R or COMMAND+R on Mac)<br />
* See results of the execurted rules in you other views<br />
<br />
=== What the pros and cons of DL Query, SPARQL (with OWL entailment regime), and SQWRL===<br />
A DL Query is a OWL class expression. It<br />
* Returns results that can be superclasses, subclasses, or individuals of the class expression.<br />
* Has compact notation<br />
* Cannot use variables, therefore cannot compare values from different properties e.g., (forall all individuals ?x of class C where ?x.length = ?x.width)<br />
* Has limited sets of operators (e.g., can use regular expressions on strings but cannot do arithmetic)<br />
* Uses open-world assumption<br />
* Resolves queries relative to import closure, does not support federated queries<br />
* Is supported by any OWL reasoning system (Protege has GUI for DL queries)<br />
<br />
SPARQL query is a graph pattern. It<br />
* Can match against anything against graph patterns.<br />
* Has a rich set of operators and functions on numbers, strings, date/time, and terms<br />
* Is widely supported (although not all SPARQL engine support OWL2 entailment regime)<br />
* Can be resolved against relational databases with mappings (e.g., Ontop)<br />
* Supports federated queries across the net<br />
* Can work with OWL ontology because of formalized OWL to RDF mapping. Complex class expressions have very verbose RDF representation.<br />
<br />
SQWRL is an extension of OWL/SWRL. It<br />
* Natively understands OWL<br />
* Allows you to query for individuals only<br />
* Has an extensible collection of built-ins (including the ability to do arithmetic)<br />
* Has set operators that “close the world”<br />
* Allows comparison of values of different properties on the same individual<br />
* Is supported by Protege only<br />
* Does not support federated queries across the net</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Install_Protege5_Mac&diff=13524Install Protege5 Mac2016-05-25T00:11:34Z<p>Samsontu: </p>
<hr />
<div>= [[File:Mac-logo.jpg|50px]] Protege 5 Installation instructions for MacOSX =<br />
<br />
__TOC__<br />
<br />
<br />
'''[[Install_Protege5|Go to the main Protege 5 installation page]]'''<br />
<br />
<br />
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.<br />
<br />
== Download the ZIP file ==<br />
* Go to the [http://protege.stanford.edu/products.php#desktop-protege Products page] on the Protege website.<br />
* Click the "Download for Mac OSX" button to download the ZIP file to your machine.<br />
<br />
<br />
== Move Protege to Applications ==<br />
* Once the download completes, navigate to the folder where the ZIP file was downloaded. On a Mac, this will typically be your "Downloads" folder. Unpack it and you should see:<br />
<br />
[[File:MacOSXInstalledProtegeFolder.png]]<br />
<br />
Drag the Protege_5.0.0 folder to the Applications directory.<br />
<br />
== Launch Protege ==<br />
To launch Protege Desktop, double-click the <code>Protégé.app</code> file in the root directory of the installation (<code>Applications/Protege_5.0.0</code>).<br />
<br />
== Allow Protege to run ==<br />
The first time you will try to run the <code>Protégé.app</code>, you may get a warning:<br />
<br />
[[File:MacOXWarningProtegeApp.png]]<br />
<br />
If you get this warning, it means that your Mac's security setting doesn't allow unidentified software to run. There are several ways to allow an exception to the rule.The simplest way is to press the Control key and click on the Protégé.app icon, then choose and click on "Open" from the shortcut menu:<br />
<br />
[[File:MacOSXOpenProtegeApp.png]]<br />
<br />
You will get another warning:<br />
<br />
[[File:MacOSXRunProtegeApp.png]]<br />
<br />
Click on "Open" and Protégé.app will start. The application is saved as an exception to your security settings, and you can open it in the future by double-clicking it just as you can any registered app.<br />
<br />
For other ways of granting exception or of configuring your Mac's security setting, see Apple's support page [https://support.apple.com/kb/PH21769?locale=en_US].<br />
<br />
<!--<br />
= Troubleshooting =<br />
<br />
''Q'': ''When I double-click on the run script, nothing happens, or I see a window that comes up, and goes away!''<br />
<br />
''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]. <br />
<br />
* How to run Protege from the console on OS X:<br />
** Open Finder<br />
** Select Applications -> Utilities, then double-click on the Terminal application<br />
** In the resulting Terminal window, change to the directory where you unzipped Protege (e.g., <code>cd /Applications/Protege_5.0_beta</code>)<br />
** Type <code>sh run.command</code><br />
<br />
Then report the results back on the [http://protege.stanford.edu/support.php protege-user] mailing list.<br />
<br />
--><br />
<br />
'''[[Install_Protege5|Go to the main Protege 5 installation page]]'''</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Install_Protege5_Mac&diff=13523Install Protege5 Mac2016-05-25T00:05:23Z<p>Samsontu: /* Allow Protege to run */</p>
<hr />
<div>= [[File:Mac-logo.jpg|50px]] Protege 5 Installation instructions for MacOSX =<br />
<br />
__TOC__<br />
<br />
<br />
'''[[Install_Protege5|Go to the main Protege 5 installation page]]'''<br />
<br />
<br />
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.<br />
<br />
== Download the ZIP file ==<br />
* Go to the [http://protege.stanford.edu/products.php#desktop-protege Products page] on the Protege website.<br />
* Click the "Download for Mac OSX" button to download the ZIP file to your machine.<br />
<br />
<br />
== Move Protege to Applications ==<br />
* Once the download completes, navigate to the folder where the ZIP file was downloaded. On a Mac, this will typically be your "Downloads" folder. Unpack it and you should see:<br />
<br />
[[File:MacOSXInstalledProtegeFolder.png]]<br />
<br />
Drag the Protege_5.0.0 folder to the Applications directory.<br />
<br />
== Launch Protege ==<br />
To launch Protege Desktop, double-click the <code>Protégé.app</code> file in the root directory of the installation (<code>Applications/Protege_5.0.0</code>).<br />
<br />
== Allow Protege to run ==<br />
The first time you will try to run the <code>Protégé.app</code>, you may get a warning:<br />
<br />
[[File:MacOXWarningProtegeApp.png]]<br />
<br />
If you get this warning, it means that your Mac's security setting doesn't allow unidentified software to run. There are several ways to allow an exception to the rule.The simplest way is to press the Control key and click on the Protégé.app icon, then choose and click on "Open" from the shortcut menu:<br />
<br />
[[File:MacOSXOpenProtegeApp.png]]<br />
<br />
You will get another warning:<br />
<br />
[[File:MacOSXRunProtegeApp.png]]<br />
<br />
Click on "Open" and Protégé.app will start. The application is saved as an exception to your security settings, and you can open it in the future by double-clicking it just as you can any registered app.<br />
<br />
For other ways of granting exception or of configuring your Mac's security setting, see Apple's support page [https://support.apple.com/kb/PH21769?locale=en_US].<br />
<br />
= Troubleshooting =<br />
<br />
''Q'': ''When I double-click on the run script, nothing happens, or I see a window that comes up, and goes away!''<br />
<br />
''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]. <br />
<br />
* How to run Protege from the console on OS X:<br />
** Open Finder<br />
** Select Applications -> Utilities, then double-click on the Terminal application<br />
** In the resulting Terminal window, change to the directory where you unzipped Protege (e.g., <code>cd /Applications/Protege_5.0_beta</code>)<br />
** Type <code>sh run.command</code><br />
<br />
Then report the results back on the [http://protege.stanford.edu/support.php protege-user] mailing list.<br />
<br />
<br />
<br />
'''[[Install_Protege5|Go to the main Protege 5 installation page]]'''</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Install_Protege5_Mac&diff=13522Install Protege5 Mac2016-05-25T00:02:27Z<p>Samsontu: /* Launch Protege */</p>
<hr />
<div>= [[File:Mac-logo.jpg|50px]] Protege 5 Installation instructions for MacOSX =<br />
<br />
__TOC__<br />
<br />
<br />
'''[[Install_Protege5|Go to the main Protege 5 installation page]]'''<br />
<br />
<br />
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.<br />
<br />
== Download the ZIP file ==<br />
* Go to the [http://protege.stanford.edu/products.php#desktop-protege Products page] on the Protege website.<br />
* Click the "Download for Mac OSX" button to download the ZIP file to your machine.<br />
<br />
<br />
== Move Protege to Applications ==<br />
* Once the download completes, navigate to the folder where the ZIP file was downloaded. On a Mac, this will typically be your "Downloads" folder. Unpack it and you should see:<br />
<br />
[[File:MacOSXInstalledProtegeFolder.png]]<br />
<br />
Drag the Protege_5.0.0 folder to the Applications directory.<br />
<br />
== Launch Protege ==<br />
To launch Protege Desktop, double-click the <code>Protégé.app</code> file in the root directory of the installation (<code>Applications/Protege_5.0.0</code>).<br />
<br />
== Allow Protege to run ==<br />
The first time you will try to run the <code>Protégé.app</code>, you may get a warning:<br />
<br />
[[File:MacOXWarningProtegeApp.png]]<br />
<br />
If you get this warning, it means that your Mac's security setting doesn't allow unidentified software to run. There are several ways to allow an exception to the rule. Press the Control key and click the Protégé.app icon, then choose and click Open from the shortcut men:<br />
<br />
[[File:MacOSXOpenProtegeApp.png]]<br />
<br />
You will get another warning:<br />
<br />
[[File:MacOSXRunProtegeApp.png]]<br />
<br />
Click on "Open" and Protégé.app will start. The application is saved as an exception to your security settings, and you can open it in the future by double-clicking it just as you can any registered app.<br />
<br />
For other ways of granting exception or of configuring your Mac's security setting, see Apple's support page [https://support.apple.com/kb/PH21769?locale=en_US]<br />
<br />
= Troubleshooting =<br />
<br />
''Q'': ''When I double-click on the run script, nothing happens, or I see a window that comes up, and goes away!''<br />
<br />
''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]. <br />
<br />
* How to run Protege from the console on OS X:<br />
** Open Finder<br />
** Select Applications -> Utilities, then double-click on the Terminal application<br />
** In the resulting Terminal window, change to the directory where you unzipped Protege (e.g., <code>cd /Applications/Protege_5.0_beta</code>)<br />
** Type <code>sh run.command</code><br />
<br />
Then report the results back on the [http://protege.stanford.edu/support.php protege-user] mailing list.<br />
<br />
<br />
<br />
'''[[Install_Protege5|Go to the main Protege 5 installation page]]'''</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Install_Protege5_Mac&diff=13521Install Protege5 Mac2016-05-25T00:00:14Z<p>Samsontu: /* Allow Protege to run */</p>
<hr />
<div>= [[File:Mac-logo.jpg|50px]] Protege 5 Installation instructions for MacOSX =<br />
<br />
__TOC__<br />
<br />
<br />
'''[[Install_Protege5|Go to the main Protege 5 installation page]]'''<br />
<br />
<br />
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.<br />
<br />
== Download the ZIP file ==<br />
* Go to the [http://protege.stanford.edu/products.php#desktop-protege Products page] on the Protege website.<br />
* Click the "Download for Mac OSX" button to download the ZIP file to your machine.<br />
<br />
<br />
== Move Protege to Applications ==<br />
* Once the download completes, navigate to the folder where the ZIP file was downloaded. On a Mac, this will typically be your "Downloads" folder. Unpack it and you should see:<br />
<br />
[[File:MacOSXInstalledProtegeFolder.png]]<br />
<br />
Drag the Protege_5.0.0 folder to the Applications directory.<br />
<br />
== Launch Protege ==<br />
To launch Protege Desktop, double-click the <code>Protégé.app</code> file in the root directory of the installation (<code>Applications/Protege_5.0.0d</code>).<br />
<br />
<br />
== Allow Protege to run ==<br />
The first time you will try to run the <code>Protégé.app</code>, you may get a warning:<br />
<br />
[[File:MacOXWarningProtegeApp.png]]<br />
<br />
If you get this warning, it means that your Mac's security setting doesn't allow unidentified software to run. There are several ways to allow an exception to the rule. Press the Control key and click the Protégé.app icon, then choose and click Open from the shortcut men:<br />
<br />
[[File:MacOSXOpenProtegeApp.png]]<br />
<br />
You will get another warning:<br />
<br />
[[File:MacOSXRunProtegeApp.png]]<br />
<br />
Click on "Open" and Protégé.app will start. The application is saved as an exception to your security settings, and you can open it in the future by double-clicking it just as you can any registered app.<br />
<br />
For other ways of granting exception or of configuring your Mac's security setting, see Apple's support page [https://support.apple.com/kb/PH21769?locale=en_US]<br />
<br />
= Troubleshooting =<br />
<br />
''Q'': ''When I double-click on the run script, nothing happens, or I see a window that comes up, and goes away!''<br />
<br />
''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]. <br />
<br />
* How to run Protege from the console on OS X:<br />
** Open Finder<br />
** Select Applications -> Utilities, then double-click on the Terminal application<br />
** In the resulting Terminal window, change to the directory where you unzipped Protege (e.g., <code>cd /Applications/Protege_5.0_beta</code>)<br />
** Type <code>sh run.command</code><br />
<br />
Then report the results back on the [http://protege.stanford.edu/support.php protege-user] mailing list.<br />
<br />
<br />
<br />
'''[[Install_Protege5|Go to the main Protege 5 installation page]]'''</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=File:MacOSXRunProtegeApp.png&diff=13520File:MacOSXRunProtegeApp.png2016-05-24T23:50:36Z<p>Samsontu: </p>
<hr />
<div></div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Install_Protege5_Mac&diff=13519Install Protege5 Mac2016-05-24T23:43:50Z<p>Samsontu: /* Allow Protege to run */</p>
<hr />
<div>= [[File:Mac-logo.jpg|50px]] Protege 5 Installation instructions for MacOSX =<br />
<br />
__TOC__<br />
<br />
<br />
'''[[Install_Protege5|Go to the main Protege 5 installation page]]'''<br />
<br />
<br />
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.<br />
<br />
== Download the ZIP file ==<br />
* Go to the [http://protege.stanford.edu/products.php#desktop-protege Products page] on the Protege website.<br />
* Click the "Download for Mac OSX" button to download the ZIP file to your machine.<br />
<br />
<br />
== Move Protege to Applications ==<br />
* Once the download completes, navigate to the folder where the ZIP file was downloaded. On a Mac, this will typically be your "Downloads" folder. Unpack it and you should see:<br />
<br />
[[File:MacOSXInstalledProtegeFolder.png]]<br />
<br />
Drag the Protege_5.0.0 folder to the Applications directory.<br />
<br />
== Launch Protege ==<br />
To launch Protege Desktop, double-click the <code>Protégé.app</code> file in the root directory of the installation (<code>Applications/Protege_5.0.0d</code>).<br />
<br />
<br />
== Allow Protege to run ==<br />
The first time you will try to run the <code>Protégé.app</code>, you may get a warning:<br />
<br />
[[File:MacOXWarningProtegeApp.png]]<br />
<br />
If you get this warning, it means that your Mac's security setting doesn't allow unidentified software to run. There are several ways to allow an exception to the rule. Press the Control key and click the Protégé.app icon, then choose and click Open from the shortcut men:<br />
<br />
[[File:MacOSXOpenProtegeApp.png]]<br />
<br />
Protégé.app is saved as an exception to your security settings, and you can open it in the future by double-clicking it just as you can any registered app.<br />
<br />
For another way to grant an exception, 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:<br />
<br />
[[File:MacOSXSecurityPrefs.png]]<br />
<br />
<br />
Click on the button ''Open anyway'' and you will get to another dialog, like:<br />
<br />
[[File:MacOSXWarning2.png]]<br />
<br />
<br />
Click on ''Open'' and Protege will start.<br />
<br />
Alternatively, you may also select for the ''Allow apps downloaded from:'' the checkbox: ''Anywhere'' in the ''Security & Privacy'' preferences panel.<br />
<br />
= Troubleshooting =<br />
<br />
''Q'': ''When I double-click on the run script, nothing happens, or I see a window that comes up, and goes away!''<br />
<br />
''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]. <br />
<br />
* How to run Protege from the console on OS X:<br />
** Open Finder<br />
** Select Applications -> Utilities, then double-click on the Terminal application<br />
** In the resulting Terminal window, change to the directory where you unzipped Protege (e.g., <code>cd /Applications/Protege_5.0_beta</code>)<br />
** Type <code>sh run.command</code><br />
<br />
Then report the results back on the [http://protege.stanford.edu/support.php protege-user] mailing list.<br />
<br />
<br />
<br />
'''[[Install_Protege5|Go to the main Protege 5 installation page]]'''</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=File:MacOSXOpenProtegeApp.png&diff=13518File:MacOSXOpenProtegeApp.png2016-05-24T23:33:48Z<p>Samsontu: </p>
<hr />
<div></div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Install_Protege5_Mac&diff=13517Install Protege5 Mac2016-05-24T23:32:40Z<p>Samsontu: /* Move Protege to Applications */</p>
<hr />
<div>= [[File:Mac-logo.jpg|50px]] Protege 5 Installation instructions for MacOSX =<br />
<br />
__TOC__<br />
<br />
<br />
'''[[Install_Protege5|Go to the main Protege 5 installation page]]'''<br />
<br />
<br />
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.<br />
<br />
== Download the ZIP file ==<br />
* Go to the [http://protege.stanford.edu/products.php#desktop-protege Products page] on the Protege website.<br />
* Click the "Download for Mac OSX" button to download the ZIP file to your machine.<br />
<br />
<br />
== Move Protege to Applications ==<br />
* Once the download completes, navigate to the folder where the ZIP file was downloaded. On a Mac, this will typically be your "Downloads" folder. Unpack it and you should see:<br />
<br />
[[File:MacOSXInstalledProtegeFolder.png]]<br />
<br />
Drag the Protege_5.0.0 folder to the Applications directory.<br />
<br />
== Launch Protege ==<br />
To launch Protege Desktop, double-click the <code>Protégé.app</code> file in the root directory of the installation (<code>Applications/Protege_5.0.0d</code>).<br />
<br />
<br />
== Allow Protege to run ==<br />
The first time you will try to run the <code>Protégé.app</code>, you may get a warning:<br />
<br />
[[File:MacOXWarningProtegeApp.png]]<br />
<br />
<br />
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:<br />
<br />
[[File:MacOSXSecurityPrefs.png]]<br />
<br />
<br />
Click on the button ''Open anyway'' and you will get to another dialog, like:<br />
<br />
[[File:MacOSXWarning2.png]]<br />
<br />
<br />
Click on ''Open'' and Protege will start.<br />
<br />
Alternatively, you may also select for the ''Allow apps downloaded from:'' the checkbox: ''Anywhere'' in the ''Security & Privacy'' preferences panel.<br />
<br />
<br />
= Troubleshooting =<br />
<br />
''Q'': ''When I double-click on the run script, nothing happens, or I see a window that comes up, and goes away!''<br />
<br />
''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]. <br />
<br />
* How to run Protege from the console on OS X:<br />
** Open Finder<br />
** Select Applications -> Utilities, then double-click on the Terminal application<br />
** In the resulting Terminal window, change to the directory where you unzipped Protege (e.g., <code>cd /Applications/Protege_5.0_beta</code>)<br />
** Type <code>sh run.command</code><br />
<br />
Then report the results back on the [http://protege.stanford.edu/support.php protege-user] mailing list.<br />
<br />
<br />
<br />
'''[[Install_Protege5|Go to the main Protege 5 installation page]]'''</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Install_Protege5_Mac&diff=13516Install Protege5 Mac2016-05-24T23:22:15Z<p>Samsontu: Update page for Protege 5.0.0</p>
<hr />
<div>= [[File:Mac-logo.jpg|50px]] Protege 5 Installation instructions for MacOSX =<br />
<br />
__TOC__<br />
<br />
<br />
'''[[Install_Protege5|Go to the main Protege 5 installation page]]'''<br />
<br />
<br />
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.<br />
<br />
== Download the ZIP file ==<br />
* Go to the [http://protege.stanford.edu/products.php#desktop-protege Products page] on the Protege website.<br />
* Click the "Download for Mac OSX" button to download the ZIP file to your machine.<br />
<br />
<br />
== Move Protege to Applications ==<br />
* Once the download completes, navigate to the folder where the ZIP file was downloaded. On a Mac, this will typically be your "Downloads" folder. Unpack it. unpacked and you should see:<br />
<br />
[[File:MacOSXInstalledProtegeFolder.png]]<br />
<br />
Drag the Protege_5.0.0 folder to the Applications directory.<br />
<br />
<br />
== Launch Protege ==<br />
To launch Protege Desktop, double-click the <code>Protégé.app</code> file in the root directory of the installation (<code>Applications/Protege_5.0.0d</code>).<br />
<br />
<br />
== Allow Protege to run ==<br />
The first time you will try to run the <code>Protégé.app</code>, you may get a warning:<br />
<br />
[[File:MacOXWarningProtegeApp.png]]<br />
<br />
<br />
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:<br />
<br />
[[File:MacOSXSecurityPrefs.png]]<br />
<br />
<br />
Click on the button ''Open anyway'' and you will get to another dialog, like:<br />
<br />
[[File:MacOSXWarning2.png]]<br />
<br />
<br />
Click on ''Open'' and Protege will start.<br />
<br />
Alternatively, you may also select for the ''Allow apps downloaded from:'' the checkbox: ''Anywhere'' in the ''Security & Privacy'' preferences panel.<br />
<br />
<br />
= Troubleshooting =<br />
<br />
''Q'': ''When I double-click on the run script, nothing happens, or I see a window that comes up, and goes away!''<br />
<br />
''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]. <br />
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* How to run Protege from the console on OS X:<br />
** Open Finder<br />
** Select Applications -> Utilities, then double-click on the Terminal application<br />
** In the resulting Terminal window, change to the directory where you unzipped Protege (e.g., <code>cd /Applications/Protege_5.0_beta</code>)<br />
** Type <code>sh run.command</code><br />
<br />
Then report the results back on the [http://protege.stanford.edu/support.php protege-user] mailing list.<br />
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'''[[Install_Protege5|Go to the main Protege 5 installation page]]'''</div>Samsontuhttps://protegewiki.stanford.edu/index.php?title=Install_Protege5_Mac&diff=13511Install Protege5 Mac2016-05-24T22:59:42Z<p>Samsontu: </p>
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<div>= [[File:Mac-logo.jpg|50px]] Protege 5 Installation instructions for MacOSX =<br />
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__TOC__<br />
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'''[[Install_Protege5|Go to the main Protege 5 installation page]]'''<br />
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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.<br />
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== Download the ZIP file ==<br />
* Go to the [http://protege.stanford.edu/products.php#desktop-protege Products page] on the Protege website.<br />
* Click the "Download for Mac OSX" button to download the ZIP file to your machine.<br />
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== Move Protege to Applications ==<br />
* Once the download completes, navigate to the folder where the ZIP file was unpacked. On a Mac, this will typically be your "Downloads" folder:<br />
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[[Image:InstallP5_DownloadsFolder.png]]<br />
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Drag the Protege_5.0_beta folder to the Applications directory.<br />
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== Launch Protege ==<br />
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>).<br />
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== Allow Protege to run ==<br />
The first time you will try to run the <code>run.command</code>, you will get a warning:<br />
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[[File:MacOXWarningProtegeApp.png]]<br />
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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:<br />
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[[File:MacOSXSecurityPrefs.png]]<br />
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Click on the button ''Open anyway'' and you will get to another dialog, like:<br />
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[[File:MacOSXWarning2.png]]<br />
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Click on ''Open'' and Protege will start.<br />
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Alternatively, you may also select for the ''Allow apps downloaded from:'' the checkbox: ''Anywhere'' in the ''Security & Privacy'' preferences panel.<br />
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= Troubleshooting =<br />
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''Q'': ''When I double-click on the run script, nothing happens, or I see a window that comes up, and goes away!''<br />
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''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]. <br />
<br />
* How to run Protege from the console on OS X:<br />
** Open Finder<br />
** Select Applications -> Utilities, then double-click on the Terminal application<br />
** In the resulting Terminal window, change to the directory where you unzipped Protege (e.g., <code>cd /Applications/Protege_5.0_beta</code>)<br />
** Type <code>sh run.command</code><br />
<br />
Then report the results back on the [http://protege.stanford.edu/support.php protege-user] mailing list.<br />
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'''[[Install_Protege5|Go to the main Protege 5 installation page]]'''</div>Samsontu