Ontological Engineering
Title: Ontological Engineering
Department of Industrial and Systems Engineering: IE 500 (Section 001). Registration number 24419
Cross-listed with Department of Philosophy: PHI 598. Registration number 24350
Time: Mondays, 4-6:50pm, Fall 2013
Room: Baldy 200G, UB North Campus
Instructors: Barry Smith and Ron Rudnicki
Office hours: By appointment via email at [1] and [2]
August 26: 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
- 2. Ontology: From Philosophy to Engineering Slides
- 3. Ontology and the Semantic Web Slides
- Lab 1: Introduction to Protégé, installation, configuration, and navigation Slides
September 9: An Overview of Ontology Projects in Military Domains
- We will begin with a video 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.
- 4. How to Integrate Data Slides
- 5. Military Ontology Slides
- 6. Basic Formal Ontology (BFO) Slides
- Lab 2: Protégé, building the taxonomy, introduction to defining classes with OWL Slides
September 16: Ontology-Based Strategies for Information Engineering in the Healthcare Domains
- 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.
- 7. Informatics and Obamacare Slides
- 8. Electronic Diseases Slides
- 9. Healthcare Information Management Slides
- 10. Strategies for Data Integration Slides
- Lab 3: Protégé, defining class relationships Slides
- Lab Note: Steps to Get OWLViz to Function in Protege
- Go to the Graphviz website 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
- Install graphviz and remember the path name of the installation folder
- Open Protege and go to the File/Preferences menu option. Once open, go to the OWLViz tab.
- 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"
- Select the "OK" button.
- Open and ontology and navigate to the OWLViz tab in Protege.
- 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.
September 23: Referent Tracking: 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?
- Lab 4: Protégé, additional definitional techniques in OWL
September 30: Ontology and the Semantic Web (with Alan Ruttenberg)
- 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 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).
- Lab 5: Protégé, annotation properties, and versioning
October 7: The CUBRC - US Army Ontology Collaboration
Co-presenter: LTC William Mandrick)
- 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).
- Quiz: Protégé and OWL
October 14: An Overview of Ontology Projects in Financial Domains
Co-presenters: Charles Hoffman and Lowell Vizenor
- Lab 6: Protégé, review and advanced topics
October 21: An Overview of Ontology Projects in Manufacturing and Retail Domains
Preliminary readings
- Ontology for Project Lifecycle Management
- The Role of Foundational Ontologies in Manufacturing Domain Applications
- Manufacturing Ontologies Portal
- A Functional Ontology of Artifacts
- Ontological Characterization of Functions
- Sustainability and Interoperability
- Aspects of the Mereology of Artifacts
- Framework for Product Knowledge
- The Design Ontology
- Product Life Cycle Management
- Ontology of Brands
- Lab 7: Introduction to SPARQL, using select queries to explore DBpedia
October 28: An Overview of Ontology Projects in Task Scheduling Domains and in Alert Systems (with Moises Sudit)
- Lab 8: SPARQL, extending select queries with filters, grouping, and booleans
November 4: Ontology and Natural Language Processing (Ron Rudnicki and Jillian Chaves)
- Lab 9: SPARQL, using construct queries to add instance data
November 11: Ontology and Information Fusion Research (with James Llinas)
- Lab 10: SPARQL, updating instance data
November 18: How to Succeed in Building Ontologies on a Large Scale (Ron Rudnicki and Tanya Malyuta)
- Lab 11: Other Semantic Web tools: Ontofox, D2RQ, and RDFa
November 25: Presentations of Student Projects
- Quiz: SPARQL
December 2: Presentations of Student Projects
Background
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, transport and financial domains. Examples include:
There is an acknowledged shortage of persons with ontological engineering expertise in these and related areas.
The Course
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 course will feature occasional guest lectures by leading ontologists from Buffalo and elsewhere, including participants in on-going ontology projects.
Outcomes
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.
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 November 25),
- 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 November 25) (50%),
- 3. class presentation (30%).
For policy regarding incompletes see here
For academic integrity policy see here
For accessibility services see here
