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''': PHI 549 Ontological Engineering, Spring 2018. Cross-listed with ENG ###
+'''Title''': PHI 598 / IE 500: Ontological Engineering (Online class), Spring 2018.
-'''Registration''': Class# TBD. Registration details for off-campus students are provided under Part Time/Graduate [http://studentaccounts.buffalo.edu/tuition/spring.php here].
+[[Ontological Engineering 2018]]
-'''Instructor''': [http://ontology.buffalo.edu/smith Barry Smith]
+'''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].
+'''Instructor''': [http://ontology.buffalo.edu/smith/shortcv.htm Barry Smith]
+'''Prerequisites''': Open to all persons with an undergraduate degree.
 '''Office hours''': By appointment via email at [mailto:phismith@buffalo.edu phismith@buffalo.edu]
 == '''The Course''' ==
-The aim of the course is to provide an introduction to the methods and uses of ontological engineering, focusing on applications in
+'''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.
-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
+The course is built out of on-line video lectures, video presentations created by students, and discussion sessions covering the topics of each lecture.
-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
+'''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.
-dissemination.
+'''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).
+'''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''' ==
+==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 [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] [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] [http://ncor.buffalo.edu/2013/IE500/Videos/3-Semantic-Web.mp4 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.
+[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]
+==February 9: Introduction to Basic Formal Ontology==
-The course is built out of fifteen 3-credit-hour sessions, each consisting of an on-line video lectures, video presentations created by students, and discussion sessions covering the topics of each lecture.
+:[http://ncor.buffalo.edu/2012/BFO_Tutorial_2012.pptx Slides]
+:[http://ncor.buffalo.edu/2017/BFO-Part1.mp4 BFO Part One: Overview of BFO]
-Readings and examples of video lectures are provided below
+==February 16: Introduction to Basic Formal Ontology (Part 2)==
-Provisional outline of 2018 lectures:
+:[http://ncor.buffalo.edu/2012/BFO_Tutorial_2012.pptx Slides]
+:[http://ncor.buffalo.edu/2017/BFO-Part2.mp4 BFO Part Two: Varieties of continuant entities]
-:1. Introduction to Ontology
+==February 23: Ontology for Systems Engineering (Parts 1 and 2)==
-:2. Big Data and How to Overcome the Problems it Causes
-:3. An Introduction to Basic Formal Ontology
-:4. Use of Ontologies in Tracking Systems
-:5. How to Build an Ontology
-:6. Creating Ontologies That Work Together
-:7. Ontology and Information Engineering in the Healthcare Domain
-:8. The Science of Document Informatics
-:9. The Semantic Web
-:10. Ontology Examples
-:11. Finance Ontology
-:12. The Ontology of Plans
-:13. Presentations of Student Projects 1
-:14. Presentations of Student Projects 2
-== '''Background''' ==
+:[https://buffalo.box.com/s/3ln2y4iwcfhdikvn1xl514qtqx07qopl Slides]
-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).
+:[https://www.youtube.com/watch?v=QGmwIWmyJeg Part 1: Introduction]
-UB ontologists are involved in a variety of national and international projects in the military, healthcare, bioscience, 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.
+:[https://www.youtube.com/watch?v=9KojcxcIBJs Part 2: Suites of Ontology Modules]
-----
+==March 2: Ontology for Systems Engineering (Parts 3. 4 and 5)==
+:[https://buffalo.box.com/s/3ln2y4iwcfhdikvn1xl514qtqx07qopl Slides]
+:[https://www.youtube.com/watch?v=6yYrFcs4MFk Part 3: Functions and Capabilities]
+:[https://youtu.be/2iSCiyJrW8w Part 4: Product Life Cycle]
+:[https://www.youtube.com/watch?v=48gi_vOtb34 Part 5: Commodities, Services, Infrastructure]
+==March 9: Simple Protege Introduction==
+[https://www.youtube.com/playlist?list=PLea0WJq13cnAfCC0azrCyquCN_tPelJN1 Videos]
+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.
-=='''1: Introduction to Ontology'''==
+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.
-*'''Ontology: A Brief Introduction'''
+==March 16: Capabilities / Emotions / Diagrams ==
-: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?
-:[http://ncor.buffalo.edu/2013/IE500/1-Introduction-to-Ontology.pptx Slides]
-:[http://ncor.buffalo.edu/2013/IE500/Videos/1-Basic-Introduction.mp4 Video]
-*'''Ontology: From Philosophy to Engineering'''
+:[https://buffalo.box.com/s/7h75mycfj8aavlf06r197kgsqjf3jk1i Slides]
-:[http://ncor.buffalo.edu/2013/IE500/2-From-Philosophy-to-Engineering.ppt Slides]
+:[https://buffalo.box.com/s/9eezntwyorb4k0t5ssfbrnhori0621k9 What do IQ tests measure?]
-:[http://ncor.buffalo.edu/2013/IE500/Videos/2-Ontology-Engineering.mp4 Video]
-*'''Ontology as a Solution to the Problem of Data Integration'''
+:[https://buffalo.box.com/s/at1oopv9wm1aemgpa6ggxjmh9m6izrpi Slides]
-:We are living in a world of big data. To find our way around this world, we need to identify and integrate the data that is important to our needs. The problem is that data is collected always from different perspectives, with different levels of detail, different granularities for example of space and time, and different communities use different technologies and different terminologies when collecting their data. This session provides an introduction to the problems of data fusion.
+:[https://www.youtube.com/watch?v=18php_34s-M The Emotion Ontology]
-:[http://ncor.buffalo.edu/2013/IE500/4-How-to-integrate-data.pptx Slides]
-:[http://ncor.buffalo.edu/2013/IE500/Videos/4-Integrating-Data.mp4 Video]
-*Tanya Malyuta (CUNY): '''Ontologies vs. Data Models'''
-:[http://ncor.buffalo.edu/2013/IE500/30-Horizontal-Integration.pptx Slides]
-:[http://ncor.buffalo.edu/2013/IE500/Videos/30-Data-Models-and-Ontologies.mp4 Video]
-*Tanya Malyuta (CUNY): '''Horizontal Integration of Intelligence Data'''
-:[http://ncor.buffalo.edu/2013/IE500/31-Ontology_and_Data_Models.pptx Slides]
-:[http://ncor.buffalo.edu/2013/IE500/Videos/31-Horizontal-Integration.mp4 Video]
-----
+:[http://ontology.buffalo.edu/smith/ppt/Diagrams-and-Time.pptx Slides]
+:[https://www.youtube.com/watch?v=AaFnMesr6uQ Diagrams and Time]
-==2. An Introduction to Basic Formal Ontology==
+==March 23: Spring Recess==
+==March 30: Social Acts==
-*Why a standard ontology architecture is needed. Basic Formal Ontology (BFO) as domain-neutral common architecture for domain ontologies defined in its terms. BFO and its competitors. Building ontologies with BFO
+:[http://ontology.buffalo.edu/smith/ppt/Commanding.pptx Slides]
+:[https://www.youtube.com/watch?v=tHap_q-dUKk Commanding and Other Social Acts]
-*[http://ncor.buffalo.edu/2014/IE500/3-BFO.pptx Slides]
+:[http://ontology.buffalo.edu/14/Rijeka/Ontology-of-Documents-May-2014-Rijeka.ppt Slides]
-*[http://ncor.buffalo.edu/2014/IE500/3-BFO-Video.mp4 Video]
+:[https://www.youtube.com/watch?v=4lg4z2up6HI Document Acts and the Ontology of Social Reality]
-*[http://ncor.buffalo.edu/2014/IE500/5-BFO2_Handout.pdf Handout]
-'''Background'''
+==April 6: Organizations, Philosophy==
-*[http://www.ifomis.uni-saarland.de/bfo/ BFO website]
+:[http://ontology.buffalo.edu/16/Organigram.pdf Slides]
+:[https://www.youtube.com/watch?v=bp3B2GkgaB8 The Ontology of the Organigram]
-----
+:[Slides]
+:[https://www.youtube.com/watch?v=9zJZiFY-ZrE Metaphysics after Darwin]
-==3. Use of Ontologies in Tracking Systems ==
+:[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]
-:Presenter: [http://www.referent-tracking.com/RTU/?page=ceusters_vita Werner Ceusters]
+==April 13: Money==
-: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.
+:[http://ontology.buffalo.edu/smith/courses16/Analytic_Metaphysics/8.ppt Slides]
+:[https://www.youtube.com/watch?v=d-wmjYbcDBg Analytic Metaphysics and Money]
-*Reading: [[How to track absolutely everything]]
+:[https://buffalo.box.com/s/uvbrxdh5j5ehbjh8j7k2c003dskcyb9i Slides]
+:[https://www.youtube.com/watch?v=jBWXz-Ot0mI Debate with John Searle on Free-Standing Y-Terms]
-*'''Basics of Referent Tracking (RT)'''
+==April 20: Quantities, Terrorism==
-:[http://ncor.buffalo.edu/2013/IE500/11-Basics-of-Referent-Tracking.pptx Slides]
-:[http://ncor.buffalo.edu/2013/IE500/Videos/11-Referent-Tracking.mp4 Video]
-*'''Referent Tracking and Video Surveillance'''
+:[http://ontology.buffalo.edu/smith/ppt/Quantities-Lugano-Feb-2017.pptx Slides]
-:[http://ncor.buffalo.edu/2013/IE500/12-RT-and-Video-Surveillance.pptx Slides]
+:[https://www.youtube.com/watch?v=xVVUH00cMNY Quantities as Fiat Universals]
-:[http://ncor.buffalo.edu/2013/IE500/Videos/12-Video-Surveillance.mp4 Video]
-*'''Referent Tracking and Data Descriptions'''
+:[http://ontology.buffalo.edu/16/Ontology-of-Terrorism.pdf Slides]
-:[http://ncor.buffalo.edu/2013/IE500/13-RT-and-Data-descriptions.pptx Slides]
+:[https://www.youtube.com/watch?v=VtRM4gPl0TU The Ontology of Terrorism]
-:[http://ncor.buffalo.edu/2013/IE500/Videos/13-Data-Descriptions.mp4 Video]
-----
+==April 27: Deontics, Disease, Patient Data==
-==4. How to Build an Ontology==
+:[http://ontology.buffalo.edu/smith/ppt/documents/Deontic-Entities-Geneva-July-2016.pdf Slides]
+:[https://youtu.be/WIJJlnLLWGU Towards an Ontology of Deontic Entities]
-*'''How to build an ontology 1'''
+:[https://buffalo.box.com/s/mvpsr0lzvkfay10d8v96ifw7pdskumg9 Slides]
-:[http://ncor.buffalo.edu/2014/IE500/5-HowToBuildAnOntology-Sep2014.ppt Slides]
+:[https://youtu.be/b4kULamlFaM The Ontology of Disease]
-:[http://ncor.buffalo.edu/2014/IE500/5-HowToBuildAnOntology1-Video.mp4 Video]
-*'''Military ontology'''
+:[https://buffalo.box.com/s/9rovx4h1yfj4e46ssh498wdkn7uf99or Slides]
-:[http://ncor.buffalo.edu/2013/IE500/18-Ontology-in-the-Military.pdf Slides1]
+:[https://www.youtube.com/watch?v=gc5a0LaXaBo The Glory and Misery of Electronic Health Records ]
-:[http://ncor.buffalo.edu/2013/IE500/Videos/18-Military-Roots.mp4 Video1]
-:[http://ncor.buffalo.edu/2013/IE500/19-Operations.pdf Slides2]
-:[http://ncor.buffalo.edu/2013/IE500/Videos/19-Military-Operations.mp4 Video2]
-*'''How to build an ontology 2'''
+==May 4: Student presentations in video format==
-:[http://ncor.buffalo.edu/2014/IE500/7-HowToBuildAnOntology2-Oct2014.ppt Slides]
-:[http://ncor.buffalo.edu/2014/IE500/6-HowToBuildAnOntology2-Video.mp4 Video]
-The Airs Suite of Ontologies and their use in annotating intelligence data. Information artifacts: Publications, databases, passports, emails. The Email Ontology. Minimal Information Checklists
+: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]
-*'''An Introduction to BFO's Treatment of Information Artifacts'''
+== '''Provisional list of topics''' ==
-:[http://ncor.buffalo.edu/2013/IE500/21-IAO-and-BFO.pptx Slides
-:[http://ncor.buffalo.edu/2013/IE500/Videos/21-Information-Artifact-Ontology-BFO-roots.mp4 Video]
+: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
 ----
-==5. Ontology and Information Engineering in the Healthcare Domain==
+== '''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
+|}
+=='''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
+|}
+=='''Grading'''==
+Grading will be based on two factors:
-: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 ontology of disease, with special reference to the phenomenon of aging.
+I: understanding and criticism of the videos presented in classes 1-13
-*'''Ontology for General Medical Science'''
+All students are required to ingest the content of all videos and to take an active part in on-line discussions throughout the semester.
-:[http://ncor.buffalo.edu/2014/IE500/7-OGMS.ppt Slides]
-:[http://ncor.buffalo.edu/2014/IE500/7-OGMS-Video.mp4 Video]
-*'''Informatics and Obamacare'''
+II: preparation of a youtube video and associated documentation (including powerpoint slides and essay).
-:[http://ncor.buffalo.edu/2013/IE500/7-informatics-obamacare.ppt Slides]
-:[http://www.youtube.com/watch?v=PhW-ix-FoOQ Video]
-*'''Readings'''
+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:
-*Genomics: [http://www.biomedcentral.com/1471-2105/9/S5/S2 Gene Ontology Annotations]
+:Statement of scope of the ontology
-*Electronic Health Records: [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/ Disease and Diagnosis]
+:Summary of existing ontologies in the relevant domain
-*Biodiversity: [http://ncorwiki.buffalo.edu/index.php/Main_Page#Semantics_of_Biodiversity Semantics of Biodiversity]
+: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
-----
+'''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:
-==6. An Overview of Ontology Projects in Military Domains==
+Weighting	Assignment
+:26%    - video summaries (2% per summary)
+:14%    - forum participation
+:20%    - youtube video
+:20%    - powerpoint slides
+:20%    - essay / ontology content
-: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.
+'''Final Grades'''
-*'''BFO and the Command Post of the Future'''
+Grade	Quality Percentage
-:[http://ncor.buffalo.edu/2013/IE500/26-BFO-CPOF.pptx Slides]
+{|
-:[http://ncor.buffalo.edu/2013/IE500/Videos/26-BFO-CPOF.mp4 Video]
+|  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
+|}
-*4. How to Integrate Data [http://ncor.buffalo.edu/2013/IE500/4-How-to-integrate-data.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/4-Integrating-Data.mp4 Video]
+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.
-*5. Military Ontology [http://ncor.buffalo.edu/2013/IE500/5-Military-Ontology.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/5-Military-Ontology.mp4 Video]
-*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] [http://ncor.buffalo.edu/2013/IE500/Videos/6-BFO.mp4 Video]
-*17. Barry Smith: Space, Time and BFO [http://ncor.buffalo.edu/2013/IE500/17-Space-time-BFO.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/17-BFO-Space-Time.mp4 Video]
-*18. [http://militaryontology.org LTC William Mandrick] LTC Mandrick]: Roots of Ontology in the Military [http://ncor.buffalo.edu/2013/IE500/18-Ontology-in-the-Military.pdf Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/18-Military-Roots.mp4 Video]
-*19. LTC Mandrick: Operational Ontology: The Future of the Military Decision Making Process (MDMP) [http://ncor.buffalo.edu/2013/IE500/19-Operations.pdf Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/19-Military-Operations.mp4 Video]
-*20. Ron Rudnicki: The CUBRC - US Army Ontology Collaboration [http://ncor.buffalo.edu/2013/IE500/20-Ontologies-for-the-Intelligence-Community.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/20-AIRS-ontologies.mp4 Video]
-----
+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.
-==6. Documents and Document Acts==
+The university’s Graduate Incomplete Policy can be found [http://grad.buffalo.edu/study/progress/policylibrary.a-to-z.html#iugrade here].
-*'''What is a document?'''
+=='''Related Policies and Services'''==
-:[http://ncor.buffalo.edu/2014/IE500/8-IAO-and-Ontology-of-Documents.ppt Slides]
-:[http://ncor.buffalo.edu/2014/IE500/8-IAO-and-Ontology-of-Documents.wmv Video (to be edited)]
-*'''Document Acts and the Ontology of Social Reality'''
+'''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.
-:[https://www.youtube.com/watch?v=JWN4Uo-GjjE Video]
-:What can we do with documents? What can we do with digital documents that we can't do with paper documents?What is a diagram? How can we extend the technology of optical character recognition (OCR) to comprehend also the graphical content of documents?
+'''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].
-*'''Reading'''
+== '''Background Reading and Video Materials''' ==
-:[http://www.jbiomedsem.com/content/5/1/10 Mining images in biomedical publications]
-:[http://www.ncbi.nlm.nih.gov/pubmed/23304318 Finding and accessing diagrams in biomedical publications]
-----
+*[http://ontology.buffalo.edu/smith/articles/ontologies.htm Ontology: An Introduction]
-==7. The Semantic Web==
+*[http://ontology.buffalo.edu/smith/articles/Horizontal-integration.pdf Horizontal Integration of Warfighter Intelligence Data]
-*'''Ontology and the Semantic Web '''
+*[http://ncorwiki.buffalo.edu/index.php/Ontology_for_Intelligence,_Defense_and_Security Ontology for Intelligence, Defense and Security (2012)]
-: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 (see below). 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.
+*[http://ncorwiki.buffalo.edu/index.php/Introduction_to_Prot%C3%A9g%C3%A9 Intoduction to Protégé]
-:[http://ncor.buffalo.edu/2013/IE500/3-Ontologies-and-Semantic-Technology.pptx Slides]
+*[https://wiki.csc.calpoly.edu/OntologyTutorial/wiki/IntroductionToOntologiesWithProtege Protégé Tutorial]
-:[http://ncor.buffalo.edu/2013/IE500/Videos/3-Semantic-Web.mp4 Video]
-'''Presentations by Alan Ruttenberg'''
+*[http://protegewiki.stanford.edu/wiki/Protege4GettingStarted Getting Started with Protege 4].
-*'''Semantic Web Vision and History'''
+*[http://owl.cs.manchester.ac.uk/tutorials/protegeowltutorial Matthew Horridge's Protege-OWL Tutorial].
-:[shttp://ncor.buffalo.edu/2014/IE500/9-Vision-History.pptx Slides]
-:[http://ncor.buffalo.edu/2014/IE500/9-Vision-History.wmvVideo]
-*'''Technology of the Semantic Web'''
+*[http://militaryontology.org Military Ontology]
-:[http://ncor.buffalo.edu/2014/IE500/9-Semweb-Technical.pptx Slides]
-:[http://ncor.buffalo.edu/2014/IE500/9-Semweb-Technical.wmv Video]
-*'''Ontology and the Semantic Web'''
+*[http://ontology.buffalo.edu/smith/ Streaming video presentations and training courses in ontology]
-:[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]
-*Tim Berners Lee Scientific American Articles :
+*[http://www.sciencedirect.com/science/article/pii/S1877050913000690 Concept Analysis to Enrich Manufacturing Service Capability Models]
-*:[http://tdo.berkeley.edu/wp-content/uploads/2013/01/SemanticWeb.pdf  The Semantic Web (2001)]
-*:[http://www.scientificamerican.com/article.cfm?id=semantic-web-in-actio  The Semantic Web in Action (2007)]
-----
+*[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]

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