Introduction to Protégé: Difference between revisions

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It will begin with a brief introduction to ontology building, and to the use and importance of ontologies, with examples from medicine and defense. This will be followed by an introduction to the Web Ontology Language (OWL). The bulk of the course will consist of an interactive introduction to the use of Protégé in building an ontology. No background in the use of computer languages and programming is presupposed. All sessions will be highly interactive.  
It will begin with a brief introduction to ontology building, and to the use and importance of ontologies, with examples from medicine and defense. This will be followed by an introduction to the Web Ontology Language (OWL). The bulk of the course will consist of an interactive introduction to the use of Protégé in building an ontology. No background in the use of computer languages and programming is presupposed. All sessions will be highly interactive.  


'''SCHEDULE'''  
== SCHEDULE ==
A detailed '''schedule''' and expanded course description are provided '''[[Protégé Tutorial Schedule | here]]'''.


A detailed schedule and expanded course description is provided [[Protégé Tutorial Schedule | here]].
What follows is a detailed schedule of the two-day [http://ncorwiki.buffalo.edu/index.php/Introduction_to_Prot%C3%A9g%C3%A9 Protégé Tutorial] to be held in the University at Buffalo on August 11-12, 2012.


== PARTICIPATION ==


This tutorial allows both face-to-face and on-line participation. Participation may be for credit (with an official university transcript), or the tutorial may be audited (with a certificate of completion if needed). 
'''Saturday, August 11, 2012'''


:'''<u>For credit</u>'''
::[http://ncor.buffalo.edu/2012/Rudnicki-Protege-1.wmv Video]
:Slides
::[http://ncor.buffalo.edu/2012/Smith-Introduction.pptx Smith]
::[http://ncor.buffalo.edu/2012/Rudnicki-Protege-1.pptx Rudnicki]


:Participation in this tutorial will yield 1 credit hour; up to 3 further credit hours can be received through completion of a project under the guidance of an assigned faculty member. Projects must be completed before November 30, 2012.
:Example OWL File
::[http://ncor.buffalo.edu/2012/TutorialMonopolyOntology.owl Monology Ontology (1)]


::Registration details for University at Buffalo (UB) students taking this course for credit are [http://myub.buffalo.edu/course/public/scripts/crs_sched.cgi?switch=showclass&semester=summer&division=NON&dept=PHI&regnum=12517 here].
:9:00-9:30am  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Introduction to Ontology (Barry Smith)
:9:30-10:30am  &nbsp;&nbsp;&nbsp;&nbsp;Introduction to RDF and RDFS (Ron Rudnicki)
:10:30-10:45am &nbsp;&nbsp;Break
:10:45-12:30pm &nbsp;&nbsp;Introduction to OWL (RR)
:12:30-1:30pm  &nbsp;&nbsp;&nbsp;&nbsp;Lunch
:1:30-3:00pm  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Developing an Ontology in Protégé OWL - Classes and Properties (RR)
:3:00-3:15pm  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Break
:3:15-5:00pm  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Developing an Ontology in Protégé OWL - Axioms and Restrictions  (RR)
'''Sunday, August 12, 2012'''


::External (non-UB) participants who wish to take this course for credit, either on-line or through face-to-face participation, should write to [mailto:phismith@buffalo.edu Barry Smith] as soon as possible.
:[http://ncor.buffalo.edu/2012/Rudnicki-Protege-2.wmv Video]
:[http://ncor.buffalo.edu/2012/Rudnicki-Protege-2.pptx Slides]


::External students may wish to consider applying credit from this tutorial to the UB [http://philosophy.buffalo.edu/graduate/areas_of_study/ma_ontology/ Masters] and [http://philosophy.buffalo.edu/graduate/areas_of_study/phd_ontology/ PhD] Programs in Ontology. The University plans also an on-line Advanced Graduate Certificate Program in Ontology, to which credits for this course will also be applicable. Further details can be obtained from [mailto:phismith@buffalo.edu Barry Smith].
:Example OWL files
::[http://ncor.buffalo.edu/2012/MonopolyOntology.owl Monopology Ontology (2)]
::[http://ncor.buffalo.edu/2012/Game1.owl Monopology Game]
:9:00-10:00am &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  Protégé Tips and Plugins (RR)
:10:00-10:30am &nbsp;&nbsp;    SPARQL Query Language for RDF (RR)
:10:30-10:45am &nbsp;&nbsp;    Break
:10:45-12:15pm &nbsp;&nbsp;    SPARQL Query Language for RDF (RR)
:12:15-1:15pm &nbsp;&nbsp;&nbsp;&nbsp;    Lunch
:1:15-2:45pm &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;    Other OWL Editors - TopBraid Composer (RR)
:2:45-3:00pm &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;    Break
:3:00-5:00pm &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;    Examples of ontology resources and how you can use them (see [http://goo.gl/AY3RN Scratchpad]


:'''<u>Auditing</u> (no credit)'''
The tutorial is designed for participants having little to no experience in creating ontologies using computers. The goal is to provide a sufficiently broad covering of OWL, Protégé, and other semantic web technologies so that participants can be immediately productive and have an understanding of the range of technologies that they build upon to support their own projects.


:Auditing by UB persons is free. For external participants an auditing fee of $100 will be charged. This fee applies equally both to on-line and face-to-face participants. All those wishing to audit this tutorial should fill in the registration form provided [http://ncor.buffalo.edu/Tutorial_Registation_Form.pdf here] as soon as possible. A certificate of participation will be supplied on request, but auditing the course does not count for credit.
'''Day 1''' will begin with an introduction to the theory and best practices of ontology development delivered by Barry Smith. Following this introduction will be a survey of the Web Ontology Language (OWL) that can be used to express the content of an ontology.  The remainder of the day will turn to the more practical matter of using Protégé to write an ontology in OWL, including how to import terms from other ontologies using the [http://obi-ontology.org/page/MIREOT MIREOT] method. An example ontology will be created in this section of the course and participants will have the opportunity to acquire hands-on experience in the use of Protégé.  


== INSTRUCTIONS FOR ON-LINE PARTICIPANTS ==
'''Day 2''' will demonstrate how to enhance the capabilities of the standard version of Protégé with plugins, including the use of OWL-reasoners and the SPARQL Query Language for RDF to expand and explore ontologies. The course will conclude with a comparison of Protégé with the Free Edition of TopBraid Composer &trade; and a brief overview of common problems arising from the use of OWL to express an ontology.


On-line participants should install Protégé version 4.2 beta (as of June 13, 2012) on a machine they can use during the course. Begin installation by first registering at the Protégé site [http://protege.stanford.edu/download/register.html/ here]. After registering, download the installation file of Protégé version 4.2 from the [http://protege.cim3.net/download/4.2/installanywhere/Web_Installers/ Protégé Version 4.2 Download Page] that is appropriate for your machine. Brief, but valid, installation instructions are provided on the Download Page. 
It will familiarize participants with:  


Log-on/dial-in instructions for on-line participants will be provided be email to registered participants in due course.
:the use of the Protégé-OWL editor to create and maintain ontologies
:enhancing Protégé with plugins
:OWL reasoning and the use of the query language SPARQL
 
During the hands-on portion of the course, participants will learn how to navigate the latest version of the Protégé tool set, which supports the full OWL 2 standard.
 
'''Background Reading'''
:A short but useful introductory tutorial on Protege-OWL can be found at [http://protegewiki.stanford.edu/wiki/Protege4GettingStarted Getting Started with Protege 4].
:A more comprehensive treatment is provided in [http://owl.cs.manchester.ac.uk/tutorials/protegeowltutorial Matthew Horridge's Protege-OWL Tutorial].
:[http://ontology.buffalo.edu/smith Barry Smith's Ontology Page], including links to audio and video presentations, and a page containing [http://ontology.buffalo.edu/smith/articles/ontologies.htm introductory material on ontology].


== FACULTY BIOS ==
== FACULTY BIOS ==
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'''[http://ontology.buffalo.edu/smith Barry Smith]''' is Distinguished Professor of Philosophy in the University at Buffalo. He has published many papers on theoretical and applied ontology and is involved in multiple ontology projects in the biomedical, military and other domains.
'''[http://ontology.buffalo.edu/smith Barry Smith]''' is Distinguished Professor of Philosophy in the University at Buffalo. He has published many papers on theoretical and applied ontology and is involved in multiple ontology projects in the biomedical, military and other domains.
[[Participation Information]]

Latest revision as of 14:39, 9 August 2014

DATE: Saturday and Sunday, August 11-12, 2012.

VENUE for FACE-TO-FACE PARTICIPATION: Room14A, Basement, Baldy Hall, University at Buffalo North Campus.

FACULTY: Ron Rudnicki (CUBRC, Buffalo), Alan Ruttenberg (University at Buffalo), Barry Smith (University at Buffalo)


DESCRIPTION

This course is for absolute beginners in ontology. It provides an introduction to the Protégé 4.2 ontology editor, details of which can be found here.

It will begin with a brief introduction to ontology building, and to the use and importance of ontologies, with examples from medicine and defense. This will be followed by an introduction to the Web Ontology Language (OWL). The bulk of the course will consist of an interactive introduction to the use of Protégé in building an ontology. No background in the use of computer languages and programming is presupposed. All sessions will be highly interactive.

SCHEDULE

A detailed schedule and expanded course description are provided here.

What follows is a detailed schedule of the two-day Protégé Tutorial to be held in the University at Buffalo on August 11-12, 2012.


Saturday, August 11, 2012

Video
Slides
Smith
Rudnicki
Example OWL File
Monology Ontology (1)
9:00-9:30am       Introduction to Ontology (Barry Smith)
9:30-10:30am     Introduction to RDF and RDFS (Ron Rudnicki)
10:30-10:45am   Break
10:45-12:30pm   Introduction to OWL (RR)
12:30-1:30pm     Lunch
1:30-3:00pm       Developing an Ontology in Protégé OWL - Classes and Properties (RR)
3:00-3:15pm       Break
3:15-5:00pm       Developing an Ontology in Protégé OWL - Axioms and Restrictions (RR)

Sunday, August 12, 2012

Video
Slides
Example OWL files
Monopology Ontology (2)
Monopology Game
9:00-10:00am       Protégé Tips and Plugins (RR)
10:00-10:30am    SPARQL Query Language for RDF (RR)
10:30-10:45am    Break
10:45-12:15pm    SPARQL Query Language for RDF (RR)
12:15-1:15pm      Lunch
1:15-2:45pm        Other OWL Editors - TopBraid Composer (RR)
2:45-3:00pm        Break
3:00-5:00pm        Examples of ontology resources and how you can use them (see Scratchpad

The tutorial is designed for participants having little to no experience in creating ontologies using computers. The goal is to provide a sufficiently broad covering of OWL, Protégé, and other semantic web technologies so that participants can be immediately productive and have an understanding of the range of technologies that they build upon to support their own projects.

Day 1 will begin with an introduction to the theory and best practices of ontology development delivered by Barry Smith. Following this introduction will be a survey of the Web Ontology Language (OWL) that can be used to express the content of an ontology. The remainder of the day will turn to the more practical matter of using Protégé to write an ontology in OWL, including how to import terms from other ontologies using the MIREOT method. An example ontology will be created in this section of the course and participants will have the opportunity to acquire hands-on experience in the use of Protégé.

Day 2 will demonstrate how to enhance the capabilities of the standard version of Protégé with plugins, including the use of OWL-reasoners and the SPARQL Query Language for RDF to expand and explore ontologies. The course will conclude with a comparison of Protégé with the Free Edition of TopBraid Composer ™ and a brief overview of common problems arising from the use of OWL to express an ontology.

It will familiarize participants with:

the use of the Protégé-OWL editor to create and maintain ontologies
enhancing Protégé with plugins
OWL reasoning and the use of the query language SPARQL

During the hands-on portion of the course, participants will learn how to navigate the latest version of the Protégé tool set, which supports the full OWL 2 standard.

Background Reading

A short but useful introductory tutorial on Protege-OWL can be found at Getting Started with Protege 4.
A more comprehensive treatment is provided in Matthew Horridge's Protege-OWL Tutorial.
Barry Smith's Ontology Page, including links to audio and video presentations, and a page containing introductory material on ontology.

FACULTY BIOS

Ron Rudnicki has a background in the areas of software quality assurance, database programming, application development and data warehousing. For the last 6 years he has developed ontologies for the Biometric Identity Management Agency, Army Net-Centric Data Strategy Center of Excellence (ANCDS CoE), and the IARPA Knowledge and Discovery Program. He is currently employed as a Senior Research Scientist at CUBRC, Inc.

Alan Ruttenberg is Director of the University at Buffalo Clinical and Translational Data Exchange. He is a prominent contributor to ontology research, and especially in the use of Semantic Web technology for integrating and querying biomedical knowledge.

Barry Smith is Distinguished Professor of Philosophy in the University at Buffalo. He has published many papers on theoretical and applied ontology and is involved in multiple ontology projects in the biomedical, military and other domains.

Participation Information

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