Applied Ontology

Title: PHI 549 Applied Ontology

Faculty: Barry Smith

Registration: Class# 24197. Registration details for off-campus students are provided here 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.

• Jan 29

Introduction to Ontology Video Slides

Ontology and Logic Video Slides

• Feb 5
• Feb 12
• Feb 19
• 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: http://ontology.buffalo.edu/smith/

Example videos are provided here: https://www.youtube.com/user/hxo3nql/playlists

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.

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