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Revision as of 18:40, 24 June 2017
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 wceusters@gmail.com
- Philosophy: Barry Smith, PhD. Contact: 126 Park Hall, N Campus, by appointment only through
phismith@buffalo.edu
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 (Student Learning Outcomes) 4, 5
- Yu, A.C., "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)
- SLO 1
- Deadline for submission of topics for papers/presentations to be presented in the final class session(s)
- Arp R, Smith B, Spear AD. Building ontologies with Basic Formal Ontology. MIT Press, 2015, chapters 3-4.
September 14: Basic Formal Ontology (BS)
- SLO 2
- 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)
- SLO 7
- Exercise: Implement in Protégé terms and definitions from the September 14 assignment. Due date: October 17.
September 28: The Ontology for General Medical Science (OGMS) (BS)
- SLO 3
- Scheuermann RH, Ceusters W, Smith B. "Toward an ontological treatment of disease and diagnosis," Summit Transl Bioinform, 2009 Mar 1;2009:116-20.
October 3 (Optional extra session): Core Competency Lectures
- Venue TBA
- 5:00pm: How to Write Grants (BS)
- 6:30pm: How to Get Published in High Impact Journals (BS)
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. (WC)
- SLO 7
- For today's team exercise, class participants are required to identify how ontology methods can be of value in understanding issues related to patient well-being, for example issues of patient care and patient safety
- Deadline for submission of first drafts of papers/presentations
- 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.
October 19: Review of paper/presentation abstracts. Identification of problems (WC, BS)
- SLO 3, 7
October 26 Principles for ontology change management and upgrade in biomedical information systems (WC)
- SLO 8
- 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
- Exercise: Correct and improve the Oct. 5 assignment on the basis of insights gained in the team exercise from Oct. 12 and adhering to the principles of change management outlined on Oct. 26.
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
November 9 Team exercise: use OGMS to improve biomedical informatics resources (WC, BS)
November 16 Evaluation of ontologies (WC, BS)
- SLO 4, 6, 8
- 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.
FALL RECESS
November 30 Student presentations 1
- SLO 6, 7
December 7 Student presentations 2
- SLO 1, 4
