Advanced Biomedical Ontology

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Advanced Topics in Biomedical Ontology

Department of Biomedical Informatics and Department of Philosophy

Type of Instruction: Seminar
Class Numbers: BMI 708 SEM, PHI 637 SEM
Semester: Fall 2017

• Thursday: 4pm to 6:50pm

• Number of Credits: 3

• Course prerequisites: BMI508 or PHI548 or PHI549.

• Instructors

Biomedical Informatics: Werner Ceusters, MD. Contact: 77 Goodell Street, 5th floor, by

appointment only through

Philosophy: Barry Smith, PhD. Contact: 126 Park Hall, N Campus, by appointment only through

Course Description

The course begins with a review of the theories underlying biomedical knowledge representation and ontology. The methods and tools for applied ontology as well as the management and maintenance of biomedical ontologies will be discussed in detail, including the principles of ontological realism and the implementation thereof in the Basic Formal Ontology (BFO). Students will gain experience with the Web Ontology Language (OWL) and the limitations thereof, and with utilities to query ontologies expressed in OWL. The students will learn how to use and evaluate classifiers and their role in subsumption. They will learn both the transitive and reflexive closure of subsumption and its applied use in ontology development, maintenance and use. This course also provides an in-depth review of current theories and research underlying the development of biomedical ontologies as well as a comparative critical analysis of the major current biomedical ontologies as well as the methods and tools for biomedical ontology development, use and evaluation.

Course Organization

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.

August 31: Mainstream systems and techniques for modeling, representing and maintaining biomedical data, information and knowledge in ontologies (WC)

SLO 4, 5
Yu, A.C., "Methods in Biomedical Ontology", Journal of Biomedical Informatics 39 (2006) 252–266.
Robert Hoehndorf, Paul N. Schofield and Georgios V. Gkoutos, "The role of ontologies in biological and biomedical research: a functional perspective", Briefings in Bioinformatics, 2015, 1–12

September 7: Best practice principles for building domain ontologies, terms, and definitions (BS)

Arp R, Smith B, Spear AD. Building ontologies with Basic Formal Ontology. MIT Press, 2015, chapters 3-4.

September 14: Basic Formal Ontology (BS)

Arp R, Smith B, Spear AD. Building ontologies with Basic Formal Ontology. MIT Press, 2015, chapters 5-6.

September 21: Introduction to Protégé ontology editor and add-on tools (Neil Otte)

Web Protégé User Guide
Exercise: Implement in Protégé terms and definitions from the September 14 assignment. Due date: October 17.

September 28: The Ontology of General Medical Science (OGMS) (BS)

Scheuermann RH, Ceusters W, Smith B. "Toward an ontological treatment of disease and diagnosis." Summit Transl Bioinform, 2009 Mar 1;2009:116-20.

October 5: Using referent tracking for building ontologies (WC)

SLO 1, 2, 4, 6
Arp R, Smith B, Spear AD. Building Ontologies with Basic Formal Ontology. MIT Press, 2015, chapter 7.
Hogan WR and Ceusters W. Diagnosis, misdiagnosis, lucky guess, hearsay, and more: an ontological analysis. Journal of Biomedical Semantics 2016;7(54).
Assignment post-lecture: Read Alert fatigue and expand the OGMS with terms and definitions required for an ontology to address alert fatigue in EHRs. Due date: October 11

October 12: Team exercise: building an ontology for patient safety (WC)

Ceusters W, Capolupo M, De Moor G, Devlies J, Smith B. An Evolutionary Approach to Realism-Based Adverse Event Representations. Methods of Information in Medicine, 2011;50(1):62-73.
Souvignet J, Rodrigues JM. Toward a patient safety upper level ontology. Stud Health Technol Inform. 2015;210:160-4. Team exercise

October 19: Ontology of food, health and physical activity (BS)

SLO 3, 7

October 26 Principles for change management in ontologies and for upgrading to new ontologies in biomedical information system (WC)

Ceusters W. "Applying Evolutionary Terminology Auditing to the Gene Ontology", Journal of Biomedical Informatics 2009;42:518–529.
Ceusters W. "SNOMED CT Revisions and Coded Data Repositories: When to Upgrade?" American Medical Informatics Association 2011 Annual Symposium Proceedings, Washington DC, October 22-26, 2011:197-206
Exercises: Correct and improve the W6 assignment on the basis of insight gained in team exercise W7 and adhere to the principles of change management of W9. Due date November 8


November 2 Ontological principles for combining healthcare data in big data repositories (WC+BS)

SLO 4,5,7
Ceusters W, Hsu CY, Smith B. "Clinical Data Wrangling using Ontological Realism and Referent Tracking", International Conference on Biomedical Ontologies (ICBO 2014), CEUR Workshop Proceedings 2014;1237:27-32.

Assess the extent to which the ontology resulting from the W8 assignment can be used to facilitate combining healthcare data in big data repositories. Prior to W12 W11 Nov 9 WC+BS Team exercise: using the OGMS to improve the OMOP, case reports, guidelines, or course of illness systems SLO 3, 7 Observational Medical Outcomes Partnership Common Data Model (

W12 Nov 16 4,6,8 WC+BS Evaluation of ontologies Obrst L, Ceusters W, Mani I, Ray S, Smith B. The Evaluation of Ontologies: toward Improved Semantic Interoperability. In: Baker, Christopher J.O.; Cheung, Kei-Hoi (Eds.) Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences. Springer, Heidelberg, 2007;:139-58.


W13 Nov 30 6, 7 WC+BS Student presentations: critical review of biomedical ontology papers To be supplied

W14 Dec 7 1,4 WC+BS Student presentations: critical review of biomedical ontology papers To be supplied