Applied Ontology (2016)

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Title: PHI 549 Applied Ontology, Spring 2017

Faculty: Barry Smith

Registration: Class# 24197. Registration details for off-campus students are provided under Part Time/Graduate here.

Course Structure: This will be a three credit hour on-line graduate seminar. It will be taught through the medium of a series of 2-hour long videos incorporating presentation of powerpoint slides and question-answer sessions. Links to videos will be distributed according to the schedule below. The final session will consist be structured around youtube videos created by the students in the class.

Course Description: An ontology is a structured collection of terms used to tag data with the goal of making data deriving from heterogeneous sources more easily searchable, comparable or combinable. Ontologies allow information to be shared across communities of scientists with different sorts of expertise. The Gene Ontology, for example, allows researchers on aging to use data from cell biology, yeast biology, cancer biology, genetics, and gerontology, because all of these disciplines create data that are tagged using Gene Ontology terms. The course will provide an introduction to ontology from an application oriented point of view, focusing on the best practices for ontology development and on the development of plug-and-play ontology modules for re-use in different areas. Examples will be drawn primarily from biology and medicine, but no expertise in this disciplines is presupposed.

Schedule The link to the course video for any given week will be provided at 9am on the corresponding Sunday (as listed below). Students are required to watch the video within 48 hours of this posting. Class participants are required to post to the class email forum questions, responses and discussion comments relating to the video from the relevant week.

January 29

Introduction to Ontology Video Slides
  • A brief history of ontology
  • Semantically enhanced publishing
  • GO: The most successful ontology thus far
  • Aristotle's Metaphysics and Categories
  • The Ontological Square
  • Granular partitions
  • Aristotle vs. Kant
Ontology and Logic Video Slides
  • David Armstrong's Spreadsheet Ontology
  • Fantology: The error of assuming that logic ('F(a)') is the guide to ontological form
  • The confusion of universals and properties
  • Universals and the Boolean organization of the world of classes
  • First order logic with universal terms (FOLWUT)

February 5

The Ontology of Social Reality Video Slides
  • Speech acts
  • The money in your bank account
  • War and chess
  • Debts
  • Institutions
  • Searle's naturalism and its problems
  • Objects vs. representations
  • Hernando de Soto and The Mystery of Capital
  • Ontology of the credit crunch
Why I Am No Longer a Philosopher (or: Ontology Leaving the Mother Ship of Philosophy) Video Slides
  • How psychology became a scientific discipline independent of philosophy in the 19th century
  • Reasons for founding a new discipline The rise of ontology as an independent discipline
  • Research centers, funding, methods, journals, peer review, national and international conferences, teaching
  • Practical applications of ontology
  • Typical results of the founding of a new discipline
  • Towards a career path for ontologists

  • February 12
Why Computer Science Needs Philosophy Video,Slides
  • Today's information-driven science faces a vast new problem of data unification
  • In medicine, this problem can be of life-and-death significance
  • The organization that is HL7
  • Ontology 101: Why computer-science ontology needs common sense
  • Does France exist?
  • Why computer scientists prefer a view of ontology as conceptual modeling
  • The alternative: scientific ontologies
  • Towards ontology (science)
Ontology and the Semantic Web Video, Slides
  • Examples of Semantic Web ontologies
  • Simple syllogisms and beyond
  • Problems with XML
  • Clay Shirky: Why the Semantic Web would be a utopia
  • Blooming 'lite' ontologies
  • Why ontology requires thinking
  • To move in the right direction, the Semantic Web needs (inter alia) a guiding upper level ontology

  • Feb 19
Towards a Standard Upper Level Ontology Video, Slides
  • Scientific ontologies have special features
  • Building scientific ontologies which work together demands a common set of ontological relations
  • Basic Formal Ontology: benefits of coordination
  • Users of BFO
  • Continuants, occurrents, realizables
  • Specific dependence, generic dependence, information artifacts
  • Dispositions, roles, functions
  • Diseases and disorders: the Ontology of General Medical Science
The Universal Core: Ontology and the US Federal Government Data Integration Initiative Video, Slides, Reading
  • The DoD Net-Centric Data Strategy
  • The Universal Core (UCore) Taxonomy and Semantic Layer
  • Reasoning with OWL DL
  • Manging extension ontologies
  • Example: Command and Control
  • Information entities
  • The UCore change management process
  • How UCore SL helps

  • Feb 26
  • Mar 5
  • Mar 12
Mar 19 Spring Recess
  • Mar 26
  • Apr 2
  • Apr 9
  • Apr 16
  • Apr 23
  • Apr 20
  • May 7 Student video presentations

Example Ontologies

Information Artifact Ontology
Gene Ontology
OBO (Open Biomedical Ontologies) Foundry
The Environment Ontology
Ontology for General Medical Science

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

Further readings are provided here:

Requirements: This course is open to all persons with an undergraduate degree and some relevant experience (for example in data scientists, information engineers, terminology researchers). No prior knowledge of ontology is required. In order to receive a grade and course credit students will be required to have reviewed in a timely manner all provided videos and any accompanying recommended reading. Grading will be on the basis of contributions to the on-line class discussion forum and on the quality and content of a 20 minute youtube video (with accompanying essay and powerpoint slide deck) on some topic in the field of applied ontology. Each student will be required to create one such video for presentation in the final class session on May 8. Examples of student videos created in comparable classes in the past are available here and here.

  • Your video should be 20 minutes long; it will be graded on the basis of clarity, force of argument, and interestingness.
  • The video should be based on a powerpoint presentation of approximately 20 slides. The slides should provide a minimal amount of text (using 30 point font or above), together with accompanying graphics of data. You should not read the slides -- rather, you should use the slides as summaries of the successive points you want to make, and present these points ex tempore.
  • The video should be accompanied by an essay presenting the points you make and providing literature references, the whole amounting to at least 3000 words. A short draft of your essay should be submitted to Dr Smith by March 31 at the latest.

Class participants should communicate by email with Dr Smith to determine topic and scope of your video presentation and accompanying materials.

Grading will be based on:

1. forum participation (25%)
2. 20 minute youtube video (25%)
3. associated powerpoint slides (25%)
4. associated essay (25%)

For policy regarding incompletes see here

For academic integrity policy see here