Ontological Engineering 2014
Time: Mondays, 4-6:50pm, Fall 2014
Room: 322 Clemens, UB North Campus
Department of Industrial and Systems Engineering: IE 500 (Section 001). Registration number 12656
- Department of Computer Science and Engineering: CSE 510. Registration number 23684
- Department of Philosophy: PHI 598. Registration number 22690
- 1 The Course
- 2 Background
- 3 August 25: Introduction to Ontology
- 4 September 8: Big Data and How to Overcome the Problems it Causes
- 5 September 15 An Introduction to Basic Formal Ontology
- 6 September 22: Use of Ontologies in Tracking Systems
- 7 September 29: How to Build an Ontology
- 8 October 6: Creating Ontologies That Work Together
- 9 October 13: Ontology and Information Engineering in the Healthcare Domain
- 10 October 20: The Science of Document Informatics
- 11 October 27: The Semantic Web
- 12 November 3: Ontology Examples
- 13 November 10: Finance Ontology
- 14 November 17: The Ontology of Plans
- 15 November 24: Presentations of Student Projects 1
- 16 December 1: : Presentations of Student Projects 2
- 17 Examples of Student Projects from 2013
- 18 Guidance for Presentations and Reports
- 19 Grading and Related Policies and Services
- 20 Preliminary Reading and Video Materials
This is, as far as we know, the first ever course on Ontological Engineering to be offered in a US university. It was first taught in 2013, and videos, presentations and reading materials from the 2013 class are available here: Ontological Engineering 2013. The course provides 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 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.
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).
UB ontologists are involved in a variety of national and international projects in the military, healthcare, bioscience, 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.
August 25: Introduction to Ontology
Lab Slides and Other Materials
What is an ontology?
Some simple examples
How are ontologies used?
How do ontologies relate to databases?
What are the differences and interrelations between ontology (philosophy), ontology (science), and ontology (engineering)?
The framework we are using: Basic Formal Ontology
Background materials from last year's class
- Ontology: A Brief Introduction Slides Video
- Ontology: From Philosophy to Engineering Slides Video
- Tanya Malyuta (CUNY): Ontologies vs. Data Models Slides Video
- Tanya Malyuta (CUNY): Horizontal Integration of Intelligence Data Slides Video
September 8: Big Data and How to Overcome the Problems it Causes
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. Strategies to address these problems:
- Linked open data
- Data fusion
- More simple examples
- The Protege Ontology Editor
We outline some of the successes and failures of these different strategies, and introduce some of the features peculiar to the ontological approach underlying much of the work on data fusion taking place in UB, as a preparation for later sessions in this class.
September 15 An Introduction to Basic Formal Ontology
- Why a standard ontology architecture is needed
- An introduction to Basic Formal Ontology (BFO)
- BFO and its competitors
- Building ontologies with BFO
September 22: Use of Ontologies in Tracking Systems
Presenter: Werner Ceusters
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?
- Basics of Referent Tracking (RT) Video
- RT and Video Surveillance Video
- RT and Data descriptions Video
September 29: How to Build an Ontology
An overview of ontology research in Buffalo
How to build an ontology 1
- Military ontology
October 6: Creating Ontologies That Work Together
- The Airs Suite of Ontologies
- Annotating Intelligence Data
- Information Artifacts: Publications, databases, passports, emails
- The Email Ontology
- Minimal Information Checklists
- An Introduction to BFO's Treatment of Information Artifacts Slides Video
- [Information Ontologies for the Intelligence Community http://ncorwiki.buffalo.edu/index.php/STIDS_2013]
October 13: Ontology and Information Engineering in the Healthcare Domain
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.
- Informatics and Obamacare: Slides Video
- Electronic Diseases: Slides
- Genomics: Gene Ontology Annotations
- Electronic Health Records: Disease and Diagnosis
- Biodiversity: Semantics of Biodiversity
- Healthcare Information Management: Slides
- Strategies for Data Integration: Slides
October 20: The Science of Document Informatics
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?
- Mining images in biomedical publications
- Finding and accessing diagrams in biomedical publications
- Document Acts and the Ontology of Social Reality
Ontology projects to be discussed
October 27: The Semantic Web
Presentations by Alan Ruttenberg
- Semantic Web Vision and History [shttp://ncor.buffalo.edu/2014/IE500/9-Vision-History.pptx Slides] 
- Technology of the Semantic Web Slides Video
- The term "Semantic Web" was introduced by Tim Berners-Lee and others in the late 1990's (1, 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.
- Applications Slides
- Tim Berners Lee Scientific American Articles :
November 3: Ontology Examples
Topics will include:
November 10: Finance Ontology
- Dennis E. Wisnosky: Video
- Background slides on FIBO, the Financial Industry Business Ontology
November 17: The Ontology of Plans
The Ontology of Planning Slides
Erik Thomsen, William Duncan, Tatanya Malyuta and Barry Smith, “A Computational Framework for Living Plan Specification, Execution and Evaluation”, Proceedings of the Conference on Semantic Technology in Intelligence, Defense and Security (STIDS), George Mason University, Fairfax, VA, November 18-20, 2014.
Kym S. Pohl and Peter Morosoff, "ICODES: A Load-Planning System that Demonstrates the Value of Ontologies in the Realm of Logistical Command and Control (C2)", InterSymp-2011, Baden-Baden, Germany, 2 Aug, 2011.
Jens Pohl, "An Intelligent Supply Chain Planning and Execution Environment" Proceedings of InterSymp-2011: Baden-Baden, Germany. Aug. 2011.
Austin Tate, Towards a Plan Ontology (1996)
Austin Tate Plan Ontology Page
November 24: Presentations of Student Projects 1
1. Philip Odonkor: Energy Ontology for Net-Zero Buildings
2. Jeon-Young Kang: An Ontology for Capturing Change
3. Joana Monteiro: Victim Management Ontology
December 1: : Presentations of Student Projects 2
1. Lauren Madar: Retail Banking Ontology
2. Cameron Bosinski: Question Ontology
3. Fumiaki Toyoshima: University Ontology
4. Keith Fitzsimmons: Lathe Maintenance Ontology
Examples of Student Projects from 2013
- Jordan Feenstra and Yonatan Schreiber: Music Ontology
- Yi Yang and Jeon-Young Kang: GIS Ontology
- David Lominac: Customer Ontology
- Lucas Mesmer: Manufacturing Ontology
- Travis Allen: Twitter Ontology
- Chad Stahl: Chemical Manufacturing Ontology
- Brian Donohue and Neil Otte: Personality Ontology
- Kevin Cui: GIS Data Model Ontology
- Xinnan Peng: Manufacturing Ontology
- John Beverley: Thermodynamic Equilibrium Ontology
- Paul Poenicke: Gettier Problem Ontology
- Adam Houser: Game Artifact Ontology
- William Hughes and Michael Moskal: Unmanned Aerial Vehicle Ontology
- Kanchan Karadkar: Supply Chain Management Ontology
- Norman Sung: Musical Genre Ontology
Guidance for Presentations and Reports
- Examples of what to include
- Statement of scope of the ontology
- The true path rule
- Identification of existing ontologies
- Explanation of how your ontology differs from (or incorporates) these
- Screenshots of parts of the ontology with some examples of important terms and definitions
- Summaries of potential applications of the ontology
Grading and Related Policies and Services
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.
For 3 credit hour students, your grade will be determined in five equal portions deriving from:
- 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 December 2),
- 4. Protégé ontology file (deadline November 25),
- 5. class presentation.
For 2 credit hour students, your grade is determined as follows:
- 1. class participation (1.5% per class attended),
- 2. written description of ontology project (4000 words; deadline December 2) (50%),
- 3. class presentation (30%).
For policy regarding incompletes see here
For academic integrity policy see here
For accessibility services see here