Biomedical Ontology 2016

Faculty:

PHI 548. Cross-listed with BMI 508

Time: 4:00-6:50pm, Mondays, Fall Semester 2016

Room: Baldy 200-G, UB North Campus

Instructors: Barry Smith (Philosophy) and Werner Ceusters (Biomedical Informatics)

Office hours: BS: Tuesdays, 12:15-1pm in 126 Park Hall and by appointment via email to [1]; WC:

3 Credit Hours

Schedule

BMI 508: Biomedical Ontology (3 credits)

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

9/19/2016 Ontology of Experiments

The generation & dissemination of new knowledge through biomedical research and clinical trials

9/26/2016 Ontology of Clinical Practice

Electronic Health Records and other systems and techniques for modeling, representing & maintaining patient data

10/3/2016 The Gene Ontology and the Open Biomedical Ontologies Foundry

History and current theoretical foundations for the development of effective biomedical ontologies

10/10/2016 Using Ontologies to Represent of Biomedical Data, Information and Knowledge

Review of the logical principles for building consistent, structured ontological representations capable of interpretation by both humans and computers==

11/21/2016 Ontology of Social Entities

Representation of race, gender, and other demographic entities; patient consent; healthcare organizations

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)

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