Biomedical Ontology 2016
Faculty: Barry Smith (Philosophy) and Werner Ceusters (Biomedical Informatics)
PHI 548 Cross-listed with BMI 508
Baldy 200-G
Fall Semsters 2016
Mondays, 4:00-6:50pm
3 Credit Hours
Schedule
BMI 508: Biomedical Ontology (3 credits)
Time: Tuesdays, 1-3:50pm, Spring 2016
Room: 141 Park Hall, UB North Campus
Instructor: Barry Smith
Office hours: Tuesdays, 12:15-1pm and by appointment via email to [1]
Course Description: This course provides an introduction to biomedical ontology. It will review how data and information are generated through biological and biomedical experimentation and patient care, and show how ontologies are used in accessing, maintaining and exploiting these data and information. It will show how biomedical ontologies are developed and provide a comparative critical analysis of major current biomedical ontologies as well as the methods and tools for biomedical ontology development and evaluation.
Course Outline: The course begins with a review of the biomedical/clinical research and information dissemination system that results in the generation of new knowledge and its dissemination into clinical health care practice. This review will also include the current systems and techniques that have been used to model, represent & maintain our biomedical data, information & knowledge for use by clinicians and researchers. The remainder of the course will provide an in-depth review of current theories, methods and tools for the development of ontologies for the organization and management of biomedical data, information & knowledge as well as a critical comparative analysis of the major current biomedical ontologies used in health care and biomedical research settings.
Recommended background reading
- R. Arp, B. Smith, A. D. Spear, Building Ontologies with Basic Formal Ontology
9/5/2016 Labor Day (no class)
9/12/2016 Introduction to Ontology
9/19/2016 The generation & dissemination of new knowledge via biomedical/clinical research & its publication
9/26/2016 The systems & techniques for modeling, representing & maintaining biomedical data, information and knowledge
10/3/2016 The history and current theoretical foundations for the development of effective biomedical ontologies
10/10/2016 Review of the logical principles for building consistent, structured ontological representations of biomedical data, information & knowledge, capable of interpretation by both humans and computers
10/17/2016 Building consistent, structured ontological representations of biomedical information (cont.)
10/24/2016 Introduction to the open source Protégé ontology editor and it’s add-on tools(WC)
10/31/2016 Laboratory exercises & problems
11/7/2016 The Unified Medial Language System (UMLS) and it’s Semantic Network
11/14/2016 The SNOMED clinical terminology and ontology
11/21/2016 The Gene Ontology (GO)
11/28/2016 Student presentations
12/5/2016 Student presentations
All students will be required to take an active part in class discussions throughout the semester and to prepare a paper on some relevant topic. The paper should be submitted in a draft version on or before October 31, and in final form on or before December 5. A powerpoint version will be presented in class in one or other of the two closing sessions.
Your grade will be determined in three equal portions deriving from:
- 1. class participation (2.5% per class attended)
- 2. paper (3000 words; deadline for draft: March 29; deadline for final version: May 3)
- 3. class presentation (graded according to quality of powerpoint slides, quality of delivery, and quality of response to questions)
For policy regarding incompletes see here
For academic integrity policy see here
For accessibility services see here
