Ontological Engineering: Difference between revisions

Latest revision as of 23:15, 29 June 2018

Title: PHI 598 / IE 500: Ontological Engineering (Online class), Spring 2018.

Ontological Engineering 2018

Registration:

Class#: 23854 (PHI)

Class#: 23450 (ENG)

Off-campus students: Registration details are provided under Part Time/Graduate here.

Instructor: Barry Smith

Prerequisites: Open to all persons with an undergraduate degree.

Office hours: By appointment via email at phismith@buffalo.edu

The Course

Course Description: The aim of the course is to provide an introduction to the methods and uses of ontological engineering, focusing on applications in areas such as military intelligence, healthcare, and document processing. It will provide an overview of how ontologies are created and used, together with practical experience in the development of ontologies and in the use of associated web technology standards. It will also address some of the human factors underlying the success and failure of ontology projects, including issues of ontology governance and dissemination.

The course is built out of on-line video lectures, video presentations created by students, and discussion sessions covering the topics of each lecture.

Course Structure: This will be a three credit hour on-line graduate seminar. It will be taught through the medium of a series of videos incorporating presentation of powerpoint slides and accompanying discussion sessions. The final session will be structured around youtube videos created by the students in the class.

Schedule: The link to the course video for any given week will be provided at 9am on the corresponding Friday (as listed below). Students are required to watch this video within 4 days of this posting and to send a ~200 word summary of its content before the end of this period (thus by Tuesday at 9am). This summary should be sent to phismith@buffalo.edu. In addition they should post to the class email forum any questions and comments relating to the video from the relevant week. Questions and comments may be posted at any time during the semester. Your activity on this email forum will be taken into account in determining your grade.

Text: Robert Arp, Barry Smith and Andrew Spear, Building Ontologies with Basic Formal Ontology, Cambridge, MA: MIT Press, August 2015.

Ontologies are an important tool in all areas where data is collected and described by different groups in different ways. Ontologies provide taxonomy-based computerized lexica used to describe diverse bodies of data. They thereby help to aggregate and compare data, to make data more easily discoverable, and to allow large bodies of data to be more effectively searched and analyzed. Ontologies also play an important role in the so-called Semantic Web, where the Web Ontology Language (OWL) forms a central building block in the stack of web technology standards created by the World Wide Web Consortium (W3C).

Ontology in Buffalo: UB ontologists are involved in a variety of national and international projects in the military, healthcare, bioscience, engineering, transport and financial domains. There is an acknowledged shortage of persons with ontological engineering expertise in all these fields, and in related fields such as journalism, manufacturing and government administration. UB ontologists also work closely with CUBRC, a Buffalo research, development, testing and systems integration company specializing in the areas of Data Science and Information Fusion; Chemical, Biological and Medical Sciences; and Aeronautics.

Schedule

January 28: Basic Introduction to Ontology

We will begin by addressing questions such as: What is an ontology? What are the differences and interrelations between ontology (philosophy), ontology (science), and ontology (engineering)? How are ontologies used? We will also provide an introduction to Basic Formal Ontology (BFO), focusing on a discussion of the question: What is a plan?

1. Ontology: A Brief Introduction Slides Video
2. Ontology: From Philosophy to Engineering Slides Video
3. Ontology and the Semantic Web Slides Video

February 2: Introduction to Ontology for Engineers

Part 1: Begins with some historical background on the growth of ontology as a discipline on the borderlines of computer science, data science and philosophy. Sketches the development of the Semantic Web and the use of ontologies in the biomedical domain. Concludes with some reflections on the problems associated with the idea of 'linked open data'.

Part 2: Begins with an outline of Basic Formal Ontology, now used as top-level architecture in more than 200 ontology development projects, across a variety of domains, including engineering. Shows how BFO can be applied to the understanding of the opposition between services and commodities, and also to the understanding of the settings in which services and commodities are sold, delivered, used, maintained, and so forth. Settings in BFO terms are sites, and this allows us to extend our approach to a treatment of the ontology of real estate. The presentation concludes with a discussion of a draft Product Life Cycle Ontology developed within the framework of the NIST Industry Ontology Foundry.

@@ Line 1: / Line 1: @@
-'''Title: Ontological Engineering'''
+'''Title''': PHI 598 / IE 500: Ontological Engineering (Online class), Spring 2018.
-Department of Industrial and Systems Engineering: IE 500 (Section 001). Registration number 24419
+[[Ontological Engineering 2018]]
-Cross-listed with Department of Philosophy: PHI 598. Registration number 24350
+'''Registration''':
+:Class#: [http://www.buffalo.edu/class-schedule?switch=showclass&semester=spring&division=GRAD&dept=PHI&regnum=23854 23854] (PHI)
+:Class#: [http://www.buffalo.edu/class-schedule?switch=showclass&semester=spring&division=GRAD&dept=IE&regnum=23450 23450] (ENG)
+:Off-campus students: Registration details are provided under Part Time/Graduate [http://studentaccounts.buffalo.edu/tuition/spring.php here].
-'''Time''': Mondays, 4-6:50pm, Fall 2013
+'''Instructor''': [http://ontology.buffalo.edu/smith/shortcv.htm Barry Smith]
-'''Room''': Baldy 200G, UB North Campus
+'''Prerequisites''': Open to all persons with an undergraduate degree.
-'''Instructors''': [http://ontology.buffalo.edu/smith Barry Smith] and [http://org.buffalo.edu/rarp/rudnicki_vita.html Ron Rudnicki]
+'''Office hours''': By appointment via email at [mailto:phismith@buffalo.edu phismith@buffalo.edu]
-'''Office hours''': By appointment via email at [mailto:phismith@buffalo.edu] and [mailto:rudnicki@cubrc.org]
+== '''The Course''' ==
+'''Course Description:''' The aim of the course is to provide an introduction to the methods and uses of ontological engineering, focusing on applications in areas such as military intelligence, healthcare, and document processing. It will provide an overview of how ontologies are created and used, together with practical experience in the development of ontologies and in the use of associated web technology standards. It will also address some of the human factors underlying the success and failure of ontology projects, including issues of ontology governance and dissemination.
+The course is built out of on-line video lectures, video presentations created by students, and discussion sessions covering the topics of each lecture.
+'''Course Structure:''' This will be a three credit hour on-line graduate seminar. It will be taught through the medium of a series of videos incorporating presentation of powerpoint slides and accompanying discussion sessions. The final session will be structured around youtube videos created by the students in the class.
+'''Schedule:''' The link to the course video for any given week will be provided at 9am on the corresponding Friday (as listed below). Students are required to watch this video within 4 days of this posting and to send a ~200 word summary of its content before the end of this period (thus by Tuesday at 9am). This summary should be sent to phismith@buffalo.edu. In addition they should post to the class email forum any questions and comments relating to the video from the relevant week. Questions and comments may be posted at any time during the semester. Your activity on this email forum will be taken into account in determining your grade.
+'''Text:''' Robert Arp, Barry Smith and Andrew Spear, [https://mitpress.mit.edu/index.php?q=books/building-ontologies-basic-formal-ontology Building Ontologies with Basic Formal Ontology], Cambridge, MA: MIT Press, August 2015.
+'''Ontologies''' are an important tool in all areas where data is collected and described by different groups in different ways. Ontologies provide taxonomy-based computerized lexica used to describe diverse bodies of data. They thereby help to aggregate and compare data, to make data more easily discoverable, and to allow large bodies of data to be more effectively searched and analyzed. Ontologies also play an important role in the so-called Semantic Web, where the Web Ontology Language (OWL) forms a central building block in the stack of web technology standards created by the World Wide Web Consortium (W3C).
-<u>[[For Lab sessions]]</u>
+'''Ontology in Buffalo''': UB ontologists are involved in a variety of national and international projects in the military, healthcare, bioscience, engineering, transport and financial domains. There is an [http://www.academia.edu/2824018/Creating_the_ontologists_of_the_future acknowledged shortage] of persons with ontological engineering expertise in all these fields, and in related fields such as journalism, manufacturing and government administration. UB ontologists also work closely with [http://www.cubrc.org/index.php/data-science-and-information-fusion/ontology CUBRC], a Buffalo research, development, testing and systems integration company specializing in the areas of Data Science and Information Fusion; Chemical, Biological and Medical Sciences; and Aeronautics.
-----
+== '''Schedule''' ==
-==August 26: Basic Introduction to Ontology ==
+==January 28: Basic Introduction to Ontology ==
-*[http://ncor.buffalo.edu/2013/IE500/Videos/IE500-Video1.m4v Video]
 *We will begin by addressing questions such as: What is an ontology? What are the differences and interrelations between ontology (philosophy), ontology (science), and ontology (engineering)? How are ontologies used? We will also provide an introduction to Basic Formal Ontology (BFO), focusing on a discussion of the question: What is a plan?
-*1. Ontology: A Brief Introduction [http://ncor.buffalo.edu/2013/IE500/1-Introduction-to-Ontology.pptx Slides]
+*1. Ontology: A Brief Introduction [http://ncor.buffalo.edu/2013/IE500/1-Introduction-to-Ontology.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/1-Basic-Introduction.mp4 Video]
-*2. Ontology: From Philosophy to Engineering [http://ncor.buffalo.edu/2013/IE500/2-From-Philosophy-to-Engineering.ppt Slides]
+*2. Ontology: From Philosophy to Engineering [http://ncor.buffalo.edu/2013/IE500/2-From-Philosophy-to-Engineering.ppt Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/2-Ontology-Engineering.mp4 Video]
-*3. Ontology and the Semantic Web [http://ncor.buffalo.edu/2013/IE500/3-Ontologies-and-Semantic-Technology.pptx Slides]
+*3. Ontology and the Semantic Web [http://ncor.buffalo.edu/2013/IE500/3-Ontologies-and-Semantic-Technology.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/3-Semantic-Web.mp4 Video]
-*Lab 1: Introduction to Protégé, installation, configuration, and navigation [http://ncor.buffalo.edu/2013/IE500/Labs/Lab-1.pptx Slides]
+==February 2: Introduction to Ontology for Engineers==
-----
+Part 1: Begins with some historical background on the growth of ontology as a discipline on the borderlines of computer science, data science and philosophy. Sketches the development of the Semantic Web and the use of ontologies in the biomedical domain. Concludes with some reflections on the problems associated with the idea of 'linked open data'.
+Part 2: Begins with an outline of Basic Formal Ontology, now used as top-level architecture in more than 200 ontology development projects, across a variety of domains, including engineering. Shows how BFO can be applied to the understanding of the opposition between services and commodities, and also to the understanding of the settings in which services and commodities are sold, delivered, used, maintained, and so forth. Settings in BFO terms are sites, and this allows us to extend our approach to a treatment of the ontology of real estate. The presentation concludes with a discussion of a draft Product Life Cycle Ontology developed within the framework of the NIST Industry Ontology Foundry.
+[https://buffalo.app.box.com/s/sus1inb6h62u8ifefjjytfummqirqq0c Slides]
+[https://www.youtube.com/watch?v=Gh0f2Us0hr0 Video Part 1],
+[https://www.youtube.com/watch?v=HDARyJBvnuc Video Part 2]
-==September 9: An Overview of Ontology Projects in Military Domains==
+==February 9: Introduction to Basic Formal Ontology==
-*[http://ncor.buffalo.edu/2013/IE500/Videos/IE500-Video2.m4v Video]
+:[http://ncor.buffalo.edu/2012/BFO_Tutorial_2012.pptx Slides]
+:[http://ncor.buffalo.edu/2017/BFO-Part1.mp4 BFO Part One: Overview of BFO]
-*We will begin with a video [http://www.youtube.com/watch?v=OzW3Gc_yA9A Introduction to Semantic Technology in the DoD Business Mission Area] by Denis Wisnosky]. We will then describe how ontology is being used for the horizontal integration of warfighter intelligence data within the framework of the US Army’s Distributed Common Ground System Standard Cloud (DSC) initiative. We outline how ontologies are being applied to bring about what we call the ‘semantic enhancement’ of data models used within each intelligence discipline. We then show how the strategy can help to overcome tendencies to stovepiping of intelligence data, and thus to help connecting the dots across different information sources.
+==February 16: Introduction to Basic Formal Ontology (Part 2)==
-*4. How to Integrate Data [http://ncor.buffalo.edu/2013/IE500/4-How-to-integrate-data.pptx Slides]
+:[http://ncor.buffalo.edu/2012/BFO_Tutorial_2012.pptx Slides]
-*5. Military Ontology [http://ncor.buffalo.edu/2013/IE500/5-Military-Ontology.pptx Slides]
+:[http://ncor.buffalo.edu/2017/BFO-Part2.mp4 BFO Part Two: Varieties of continuant entities]
-*6. [http://ncorwiki.buffalo.edu/index.php/Basic_Formal_Ontology_2.0 Basic Formal Ontology] (BFO) [http://ncor.buffalo.edu/2013/IE500/6-BFO.pptx Slides]
-*Lab 2: Protégé, building the taxonomy, introduction to defining classes with OWL [http://ncor.buffalo.edu/2013/IE500/Labs/Lab-2.pptx Slides]
+==February 23: Ontology for Systems Engineering (Parts 1 and 2)==
-----
+:[https://buffalo.box.com/s/3ln2y4iwcfhdikvn1xl514qtqx07qopl Slides]
-==September 16: Ontology-Based Strategies for Information Engineering in the Healthcare Domains==
+:[https://www.youtube.com/watch?v=QGmwIWmyJeg Part 1: Introduction]
-*Health care today rests increasingly on the proper use of data deriving from different sources (data pertaining to genes, diseases, symptoms, drugs, medical devices, procedures, hospital infections and other adverse events, hospital management, billing, reporting, and many more). We provide an introduction to the world of healthcare data management, with special emphasis on the role of ontologies and standard terminologies.
+:[https://www.youtube.com/watch?v=9KojcxcIBJs Part 2: Suites of Ontology Modules]
-*7. Informatics and Obamacare [http://ncor.buffalo.edu/2013/IE500/7-informatics-obamacare.ppt Slides]
+==March 2: Ontology for Systems Engineering (Parts 3. 4 and 5)==
-*8. Electronic Diseases [http://ncor.buffalo.edu/2013/IE500/8-e-Iatrogenesis.pptx Slides]
-*9. Healthcare Information Management [http://ncor.buffalo.edu/2013/IE500/9-Healthcare-Information-Management.ppt Slides]
-*10. Strategies for Data Integration [http://ncor.buffalo.edu/2013/IE500/10-Strategies%20for%20Data%20Integration.pptx Slides]
-*Lab 3: Protégé, defining class relationships [http://ncor.buffalo.edu/2013/IE500/Labs/Lab-3.pptx Slides]
+:[https://buffalo.box.com/s/3ln2y4iwcfhdikvn1xl514qtqx07qopl Slides]
+:[https://www.youtube.com/watch?v=6yYrFcs4MFk Part 3: Functions and Capabilities]
-*'''Lab Note: Steps to Get OWLViz to Function in Protege'''
+:[https://youtu.be/2iSCiyJrW8w Part 4: Product Life Cycle]
+:[https://www.youtube.com/watch?v=48gi_vOtb34 Part 5: Commodities, Services, Infrastructure]
-:a. Go to the Graphviz website [http://www.graphviz.org/Download..php Graphviz Downloads] and select the installer package that is appropriate for your machine. For Windows, this is the Microsoft installer file: graphviz-2.34.msi
+==March 9: Simple Protege Introduction==
-:b. Install graphviz and remember the path name of the installation folder
-:c. Open Protege and go to the File/Preferences menu option. Once open, go to the OWLViz tab.
-:d. Manually enter or use the browse button to select the Dot Application Path to the dot.exe file. If your path name contains a space, include the entire name in double quotation marks: "C:\Program Files\Graphviz2.34\bin\dot.exe"
-:e. Select the "OK" button.
-:f. Open and ontology and navigate to the OWLViz tab in Protege.
-:g. Select one of the classes in Class Hierarchy and confirm that you can see a graph of the class including it's parent and children classes.
-----
+[https://www.youtube.com/playlist?list=PLea0WJq13cnAfCC0azrCyquCN_tPelJN1 Videos]
-==September 23: Referent Tracking: Use of Ontologies in Tracking Systems ==
+When watching these videos please bear in mind that we have not introduced in the class so far the specific terminology used by Protege. Most importantly, 'class' in Sadawi's course is what we have been referring to as 'type' or 'universal'. 'Property' is what we have been referring to as 'Relation'. Each property has a domain and a range; for instance the property teaches has the domain teacher and the range student. A guide (probably more than you need) is [https://www.w3.org/TR/owl-guide/ here] and there is also an introduction to the Semantic Web in the Appendix to the BFO book. If there is terminology used in Sadawi's lectures which you think needs explaining please feel free to post a request to the the class email list.
-[[Dial-in instructions]]
+In addition to taking Sadawi's course, the task for this week is to download Protege to your computer from [https://protege.stanford.edu/ here] and experiment with creating a simple ontology of your own and posting it to the class list. This ontology should relate to the topic you have selected for your final class presentation.
-*Presenter: [http://www.referent-tracking.com/RTU/?page=ceusters_vita Werner Ceusters]
+==March 16: Capabilities / Emotions / Diagrams ==
-*11. [http://ncor.buffalo.edu/2013/IE500/11-Basics-of-Referent-Tracking.pptx Basics of Referent Tracking (RT)]
+:[https://buffalo.box.com/s/7h75mycfj8aavlf06r197kgsqjf3jk1i Slides]
-*12. [http://ncor.buffalo.edu/2013/IE500/12-RT-and-Video-Surveillance.pptx RT and Video Surveillance]
+:[https://buffalo.box.com/s/9eezntwyorb4k0t5ssfbrnhori0621k9 What do IQ tests measure?]
-*13. [http://ncor.buffalo.edu/2013/IE500/13-RT-and-Data-descriptions.pptx RT and Data descriptions]
-*A referent tracking system (RTS) is a special kind of digital information system that is designed to keep track of both (1) what is the case in reality and (2) what is expressed in other information systems about what is believed to be the case in reality. An RTS also keeps track of how changes in the information system correspond to changes in the reality outside that system. We will provide an introduction to referent tracking and its implementations. Reading: [[How to track absolutely everything?]]
+:[https://buffalo.box.com/s/at1oopv9wm1aemgpa6ggxjmh9m6izrpi Slides]
+:[https://www.youtube.com/watch?v=18php_34s-M The Emotion Ontology]
-*Lab 4: Protégé, additional definitional techniques in OWL [http://ncor.buffalo.edu/2013/IE500/Labs/Lab-4.pptx Slides]
+:[http://ontology.buffalo.edu/smith/ppt/Diagrams-and-Time.pptx Slides]
-*[[http://ncor.buffalo.edu/2013/IE500/Labs/Widget-Ontology.owl Widget Ontology]
+:[https://www.youtube.com/watch?v=AaFnMesr6uQ Diagrams and Time]
-----
+==March 23: Spring Recess==
+==March 30: Social Acts==
-==September 30: Ontology and the Semantic Web (with [http://sciencecommons.org/about/whoweare/ruttenberg/ Alan Ruttenberg])==
+:[http://ontology.buffalo.edu/smith/ppt/Commanding.pptx Slides]
+:[https://www.youtube.com/watch?v=tHap_q-dUKk Commanding and Other Social Acts]
-* The term "Semantic Web" was introduced by Tim Berners-Lee and others in the late 1990's  ([http://www.w3.org/DesignIssues/Overview.html 1], [http://www.w3.org/DesignIssues/Semantic.html 2]) and first popularized in a paper in 2001 in Scientific American [http://purl.org/net/tsw 3]. Berners-Lee summarizes the idea as "a web of data that can be processed directly and indirectly by machines.", an extension of the web of documents primarily intended for consumption by people. We will discuss the goals of the Semantic Web, current technologies, some technological/intellectual sub-communities, and review some applications in biomedicine and other fields.  Topics to be discussed will include: Linked Open Data, The role of ontology, URIs, RDF, OWL, SPARQL, triple stores, and the World Wide WEB Consortium (W3C).
+:[http://ontology.buffalo.edu/14/Rijeka/Ontology-of-Documents-May-2014-Rijeka.ppt Slides]
+:[https://www.youtube.com/watch?v=4lg4z2up6HI Document Acts and the Ontology of Social Reality]
-*Lab 5: Protégé, annotation properties, and versioning
+==April 6: Organizations, Philosophy==
-==October 7: The CUBRC - US Army Ontology Collaboration==
+:[http://ontology.buffalo.edu/16/Organigram.pdf Slides]
+:[https://www.youtube.com/watch?v=bp3B2GkgaB8 The Ontology of the Organigram]
-Co-presenter: [http://militaryontology.org LTC William Mandrick])
+:[Slides]
+:[https://www.youtube.com/watch?v=9zJZiFY-ZrE Metaphysics after Darwin]
-*LTC Mandrick will describe the roots of ontology in the military. He will discuss the role of ontology and computation in the future of the Military Decision Making Process (MDMP).
+:[https://www.buffalo.edu/capenchair/events/lectures/barry-smith.html Slides]
+:[https://www.youtube.com/watch?v=YkYlY2jnRxc The Future of the History of Philosophy]
-*Quiz: Protégé and OWL
+==April 13: Money==
-==October 14: An Overview of Ontology Projects in Financial Domains==
+:[http://ontology.buffalo.edu/smith/courses16/Analytic_Metaphysics/8.ppt Slides]
+:[https://www.youtube.com/watch?v=d-wmjYbcDBg Analytic Metaphysics and Money]
-Co-presenters: [http://xbrl.squarespace.com/about-the-author/ Charles Hoffman] and [http://www.linkedin.com/in/lowellvizenor Lowell Vizenor]
+:[https://buffalo.box.com/s/uvbrxdh5j5ehbjh8j7k2c003dskcyb9i Slides]
+:[https://www.youtube.com/watch?v=jBWXz-Ot0mI Debate with John Searle on Free-Standing Y-Terms]
-*Lab 6: Protégé, review and advanced topics
+==April 20: Quantities, Terrorism==
-==October 21: An Overview of Ontology Projects in Manufacturing and Retail Domains==
+:[http://ontology.buffalo.edu/smith/ppt/Quantities-Lugano-Feb-2017.pptx Slides]
+:[https://www.youtube.com/watch?v=xVVUH00cMNY Quantities as Fiat Universals]
-''Preliminary readings''
+:[http://ontology.buffalo.edu/16/Ontology-of-Terrorism.pdf Slides]
-:[http://ontoplm.wordpress.com/call-for-papers/ Ontology for Project Lifecycle Management]
+:[https://www.youtube.com/watch?v=VtRM4gPl0TU The Ontology of Terrorism]
-:[http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.165.3067&rep=rep1&type=pdf The Role of Foundational Ontologies in Manufacturing Domain Applications]
-:[http://www.nist.gov/manufacturing-ontologies-portal.cfm Manufacturing Ontologies Portal]
-:[http://ncor.buffalo.edu/2013/Readings/Mizoguchi.doc A Functional Ontology of Artifacts]
-:[http://www.ei.sanken.osaka-u.ac.jp/pub/documents/kita-aiedam2013.pdf Ontological Characterization of Functions]
-:[http://hal.archives-ouvertes.fr/docs/00/85/77/94/PDF/Susta_Interop_EI2N2013_v3_final.pdf Sustainability and Interoperability]
-:[https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnxwZXRlcm1zaW1vbnN8Z3g6MmY0YmVjNThiYjM1N2VmZA Aspects of the Mereology of Artifacts]
-:[http://smartcustomization.mit.edu/images/MCPC%202003/site/3-MCP%20Product%20Design/15-Riis.pdf Framework for Product Knowledge]
-:[http://www.academia.edu/1265169/The_Design_Ontology_Foundation_for_the_Design_Knowledge_Exchange_and_Management The Design Ontology]
-:[http://en.wikipedia.org/wiki/Product_lifecycle_management Product Life Cycle Management]
-:[http://ontology.buffalo.edu/brands.html Ontology of Brands]
-*Lab 7: Introduction to SPARQL, using select queries to explore DBpedia
+==April 27: Deontics, Disease, Patient Data==
-<u>October 28: An Overview of Ontology Projects in Task Scheduling Domains and in Alert Systems (with Moises Sudit)</u>
+:[http://ontology.buffalo.edu/smith/ppt/documents/Deontic-Entities-Geneva-July-2016.pdf Slides]
+:[https://youtu.be/WIJJlnLLWGU Towards an Ontology of Deontic Entities]
-*Lab 8: SPARQL, extending select queries with filters, grouping, and booleans
+:[https://buffalo.box.com/s/mvpsr0lzvkfay10d8v96ifw7pdskumg9 Slides]
+:[https://youtu.be/b4kULamlFaM The Ontology of Disease]
-<u>November 4: Ontology and Natural Language Processing (Ron Rudnicki and Jillian Chaves)</u>
+:[https://buffalo.box.com/s/9rovx4h1yfj4e46ssh498wdkn7uf99or Slides]
+:[https://www.youtube.com/watch?v=gc5a0LaXaBo The Glory and Misery of Electronic Health Records ]
-*Lab 9: SPARQL, using construct queries to add instance data
+==May 4: Student presentations in video format==
-<u>November 11: Ontology and Information Fusion Research (with James Llinas)</u>
+:Hendry Davignon, [https://www.youtube.com/watch?v=42LSenEYLKw&feature=youtu.be Ontology of the US Government]
+:Timothy Schuler, [https://www.youtube.com/watch?v=22J6c0sPgHw Review of Ontologies for Malware Classification]
+:Alexander Anderson, [https://youtu.be/jFZQWwESRmw Quantum Waves in BFO]
+:Jonathan Vajda, [https://youtu.be/ifLuaBLL8f4 Ontology of the Unconscious]
-*Lab 10: SPARQL, updating instance data
+== '''Provisional list of topics''' ==
-<u>November 18: How to Succeed in Building Ontologies on a Large Scale (Ron Rudnicki and Tanya Malyuta) </u>
+:Ontology, AI and Robotics
+:Services, Commodities, Infrastructure
+:Product Life Cycle Ontology
+:Ontology and Information Engineering in the Healthcare Domain
+:The Science of Document Informatics
+:Finance Ontology
+:The Ontology of Plans
+:Ontology of Military Logistics
+:Ontology and Intelligence Analysis
+:Ontology and Data Fusion
+:Ontology of Terrorism
+----
-*Lab 11: Other Semantic Web tools: Ontofox, D2RQ, and RDFa
+== '''Student Learning Outcomes''' ==
+{| class="wikitable"
+|-
+! Program Outcomes/Competencies
+! Instructional Method(s)
+! Assessment Method(s)
+|-
+| The student will acquire a thorough knowledge of current ontology research in areas relating to engineering, data fusion, defense and intelligence
+| Video lectures and online discussions
+| Review of submitted online content and of participation in online discussion forum
+|-
+| The student will acquire experience in ontology development
+| Video lectures and critique of successive drafts
+| Review of results in the form of xsl spreadsheet or Protégé file
+|-
+| The student will acquire experience in communicating the results of work on ontology development
+| Creation of youtube presentation and of associated documentation
+| Review of results
+|}
-<u>November 25: Presentations of Student Projects</u>
+=='''Important dates'''==
+{|
+|  Jan 28 || - first video released by Dr Smith at 9am
+|-
+|   Feb 20 || - about now start to discuss by email the content of your video and essay with Dr Smith
+|-
+|   Feb 28 || - submit a proposed title and abstract
+|-
+|   Mar 16 || - create a simple ontology using Protege
+|-
+|   Mar 31 || - submit a table of contents and 300 word summary plus draft of associated ppt slides
+|-
+|   Apr 27 || - submit penultimate draft of essay and powerpoint
+|-
+|   May 4 || - submit final version of essay and powerpoint and upload final version of video to youtube
+|}
-*Quiz: SPARQL
+=='''Grading'''==
-<u>December 2: Presentations of Student Projects</u>
+Grading will be based on two factors:
-== '''Background''' ==
+I: understanding and criticism of the videos presented in classes 1-13
+All students are required to ingest the content of all videos and to take an active part in on-line discussions throughout the semester.
-Ontologies are an important tool in all areas where data is collected and described by different groups in different ways. Ontologies provide taxonomy-based computerized lexica used to describe diverse bodies of data. They thereby help to aggregate and compare data, to make data more easily discoverable, and to allow large bodies of data to be more effectively searched and analyzed. Ontologies also play an important role in the so-called Semantic Web, where the Web Ontology Language (OWL) forms a central building block in the stack of web technology standards created by the World Wide Web Consortium (W3C).
+II: preparation of a youtube video and associated documentation (including powerpoint slides and essay).
-UB ontologists are involved in a variety of national and international projects in the military, healthcare, transport and financial domains. Examples include:
+Content and structure of the essay should be discussed with Dr Smith. Where the essay takes the form of the documentation of a specific ontology developed by the student it should include:
+:Statement of scope of the ontology
+:Summary of existing ontologies in the relevant domain
+:Explanation of how your ontology differs from (or incorporates) these ontologies
+:Screenshots of parts of the ontology with some examples of important terms and definitions
+:Summaries of potential applications of the ontology
-*[http://ncor.buffalo.edu/OI2/ Information Integration in Military Intelligence]
+'''Grading Policy:''' Grading follows standard [http://grad.buffalo.edu/Academics/Policies-Procedures/Grading-Procedures.html Graduate School policies]. Grades will be weighted according to the following breakdown:
-*[http://www.youtube.com/watch?v=PWUA502hm-k Digitally Connected Medical Devices]
+Weighting	Assignment
+:26%    - video summaries (2% per summary)
+:14%    - forum participation
+:20%    - youtube video
+:20%    - powerpoint slides
+:20%    - essay / ontology content
-*[http://xbrl.squarespace.com/financial-report-ontology/ Digital Financial Reporting]
+'''Final Grades'''
-*[http://charleston.afceachapter.org/2012MarchSemantics/009%20-%20Vizenor_STS_20120321.pdf The Next Generation Air Transportation System]
+Grade	Quality Percentage
+{|
+|  A	|| 4.0	|| 93.0% -100.00%
+|-
+| A-	|| 3.67	|| 90.0% - 92.9%
+|-
+| B+	|| 3.33	|| 87.0% - 89.9%
+|-
+| B	|| 3.00	|| 83.0% - 86.9%
+|-
+| B-	|| 2.67	|| 80.0% - 82.9%
+|-
+| C+	|| 2.33	|| 77.0% - 79.9%
+|-
+| C	|| 2.00	|| 73.0% - 76.9%
+|-
+| C-	|| 1.67	|| 70.0% - 72.9%
+|-
+| D+	|| 1.33	|| 67.0% - 69.9%
+|-
+| D	|| 1.00	|| 60.0% - 66.9%
+|-
+| F	|| 0	|| 59.9% or below
+|}
-There is an [http://www.academia.edu/2824018/Creating_the_ontologists_of_the_future acknowledged shortage] of persons with ontological engineering expertise in these and related areas.
+An interim grade of Incomplete (I) may be assigned if the student has not completed all requirements for the course. An interim grade of 'I' shall not be assigned to a student who did not attend the course. The default grade accompanying an interim grade of 'I' shall be 'U' and will be displayed on the UB record as 'IU.' The default Unsatisfactory (U) grade shall become the permanent course grade of record if the 'IU' is not changed through formal notice by the instructor upon the student's completion of the course.
-== '''The Course''' ==
+Assignment of an interim 'IU' is at the discretion of the instructor. A grade of 'IU' can be assigned only if successful completion of unfulfilled course requirements can result in a final grade better than the default 'U' grade. The student should have a passing average in the requirements already completed. The instructor shall provide the student specification, in writing, of the requirements to be fulfilled.
-This is, as far as we know, the first ever course on Ontological Engineering to be offered in a US university. It will provide an introduction to the methods and uses of ontological engineering, focusing on applications in the areas of military intelligence, healthcare, and finance. It will provide an overview of how ontologies are created and used, together with practical experience in the development of OWL ontologies and in the use of associated web technology standards. It will also address some of the human factors underlying the success and failure of ontology projects, including issues of ontology governance and dissemination.
-The course will be built out of 3-hour sessions, each of which will involve 2 hours of lecturing and discussion and 1 hour of practical experience with ontology editing software and other semantic web technologies. Students may elect to take the course for 2 credit hours without the practical segment.
+The university’s Graduate Incomplete Policy can be found [http://grad.buffalo.edu/study/progress/policylibrary.a-to-z.html#iugrade here].
-The course will feature occasional guest lectures by leading ontologists from Buffalo and elsewhere, including participants in on-going ontology projects.
+=='''Related Policies and Services'''==
-----
+'''Academic integrity''' is a fundamental university value. Through the honest completion of academic work, students sustain the integrity of the university while facilitating the university's imperative for the transmission of knowledge and culture based upon the generation of new and innovative ideas. See http://grad.buffalo.edu/Academics/Policies-Procedures/Academic-Integrity.html.
-== '''Outcomes''' ==
+'''Accessibility resources:''' If you have any disability which requires reasonable accommodations to enable you to participate in this course, please contact the Office of Accessibility Resources in 60 Capen Hall, 645-2608 and also the instructor of this course during the first week of class. The office will provide you with information and review appropriate arrangements for reasonable accommodations, which can be found on the web [http://www.buffalo.edu/studentlife/who-we-are/departments/accessibility.html here].
+== '''Background Reading and Video Materials''' ==
-By the end of the class, students will be able to understand the nature, utility and scope of contemporary ontological engineering. They will understand methods and rules for ontology development; gain experience of what is involved in contributing to ontological initiatives, and learn to understand the benefits and risks of such initiatives.
+*[http://ontology.buffalo.edu/smith/articles/ontologies.htm Ontology: An Introduction]
-== '''Grading and Related Policies and Services''' ==
+*[http://ontology.buffalo.edu/smith/articles/Horizontal-integration.pdf Horizontal Integration of Warfighter Intelligence Data]
+*[http://ncorwiki.buffalo.edu/index.php/Ontology_for_Intelligence,_Defense_and_Security Ontology for Intelligence, Defense and Security (2012)]
-All students will be required to take an active part in class discussions throughout the semester. In addition they will be required to design and complete an ontology project, including written description, and brief presentation of the project in class. Students enrolled in the practical segment will be required to create a Protégé file to accompany their ontology project, and also to complete quizzes designed to gauge developing competence in the use of the Protégé Ontology Editor and SPARQL query language.
+*[http://ncorwiki.buffalo.edu/index.php/Introduction_to_Prot%C3%A9g%C3%A9 Intoduction to Protégé]
-For 3 credit hour students, your grade will be determined in five equal portions deriving from:
+*[https://wiki.csc.calpoly.edu/OntologyTutorial/wiki/IntroductionToOntologiesWithProtege Protégé Tutorial]
-:1. class participation (1.5% per class attended),
-:2. results of two quizzes relating to the lab portion of the course
-:3. written description of ontology project (3000 words; deadline November 25),
-:4. Protégé ontology file (deadline November 25),
-:5. class presentation.
-For 2 credit hour students, your grade is determined as follows:
+*[http://protegewiki.stanford.edu/wiki/Protege4GettingStarted Getting Started with Protege 4].
-:1. class participation (1.5% per class attended),
+*[http://owl.cs.manchester.ac.uk/tutorials/protegeowltutorial Matthew Horridge's Protege-OWL Tutorial].
-:2. written description of ontology project (4000 words; deadline November 25) (50%),
-:3. class presentation (30%).
-For policy regarding incompletes see [http://undergrad-catalog.buffalo.edu/policies/grading/explanation.shtml here]
+*[http://militaryontology.org Military Ontology]
-For academic integrity policy see [http://www.grad.buffalo.edu/policies/academicintegrity.php here]
+*[http://ontology.buffalo.edu/smith/ Streaming video presentations and training courses in ontology]
-For accessibility services see [http://www.buffalo.edu/accessibility/servc.php here]
+*[http://www.sciencedirect.com/science/article/pii/S1877050913000690 Concept Analysis to Enrich Manufacturing Service Capability Models]
+*[http://www.sciencedirect.com/science/article/pii/S0166361514000438 Supply Chain Management Ontology]
-== '''Preliminary Reading and Video Materials''' ==
+*[http://link.springer.com/article/10.1007/s40436-014-0073-2 Ontology-based interoperability solutions for textile supply chain]
 *[http://ontology.buffalo.edu/smith/articles/ontologies.htm Ontology: An Introduction]
@@ Line 220: / Line 312: @@
 *[http://www.sciencedirect.com/science/article/pii/S1877050913000690 Concept Analysis to Enrich Manufacturing Service Capability Models]
+*[http://www.sciencedirect.com/science/article/pii/S0166361514000438 Supply Chain Management Ontology]
+*[http://link.springer.com/article/10.1007/s40436-014-0073-2 Ontology-based interoperability solutions for textile supply chain]

Program Outcomes/Competencies	Instructional Method(s)	Assessment Method(s)
The student will acquire a thorough knowledge of current ontology research in areas relating to engineering, data fusion, defense and intelligence	Video lectures and online discussions	Review of submitted online content and of participation in online discussion forum
The student will acquire experience in ontology development	Video lectures and critique of successive drafts	Review of results in the form of xsl spreadsheet or Protégé file
The student will acquire experience in communicating the results of work on ontology development	Creation of youtube presentation and of associated documentation	Review of results

Jan 28	- first video released by Dr Smith at 9am
Feb 20	- about now start to discuss by email the content of your video and essay with Dr Smith
Feb 28	- submit a proposed title and abstract
Mar 16	- create a simple ontology using Protege
Mar 31	- submit a table of contents and 300 word summary plus draft of associated ppt slides
Apr 27	- submit penultimate draft of essay and powerpoint
May 4	- submit final version of essay and powerpoint and upload final version of video to youtube

A	4.0	93.0% -100.00%
A-	3.67	90.0% - 92.9%
B+	3.33	87.0% - 89.9%
B	3.00	83.0% - 86.9%
B-	2.67	80.0% - 82.9%
C+	2.33	77.0% - 79.9%
C	2.00	73.0% - 76.9%
C-	1.67	70.0% - 72.9%
D+	1.33	67.0% - 69.9%
D	1.00	60.0% - 66.9%
F	0	59.9% or below

Ontological Engineering: Difference between revisions

Latest revision as of 23:15, 29 June 2018

The Course

Schedule

January 28: Basic Introduction to Ontology

February 2: Introduction to Ontology for Engineers

February 9: Introduction to Basic Formal Ontology

February 16: Introduction to Basic Formal Ontology (Part 2)

February 23: Ontology for Systems Engineering (Parts 1 and 2)

March 2: Ontology for Systems Engineering (Parts 3. 4 and 5)

March 9: Simple Protege Introduction

March 16: Capabilities / Emotions / Diagrams

March 23: Spring Recess

March 30: Social Acts

April 6: Organizations, Philosophy

April 13: Money

April 20: Quantities, Terrorism

April 27: Deontics, Disease, Patient Data

May 4: Student presentations in video format

Provisional list of topics

Student Learning Outcomes

Important dates

Grading

Related Policies and Services

Background Reading and Video Materials

Navigation menu

Search